diff --git a/engine/runtime-integration-tests/src/test/scala/org/enso/compiler/test/core/ir/MetadataStorageTest.scala b/engine/runtime-integration-tests/src/test/scala/org/enso/compiler/test/core/ir/MetadataStorageTest.scala
index 1f2fdf65582a..07a0c187d29c 100644
--- a/engine/runtime-integration-tests/src/test/scala/org/enso/compiler/test/core/ir/MetadataStorageTest.scala
+++ b/engine/runtime-integration-tests/src/test/scala/org/enso/compiler/test/core/ir/MetadataStorageTest.scala
@@ -159,7 +159,7 @@ class MetadataStorageTest extends CompilerTest {
       meta1.update(TestPass1, meta)
       meta2.update(TestPass1, meta)
 
-      meta1 shouldNot equal(meta2)
+      meta1 shouldEqual meta2
     }
 
     def newMetadataStorage(init: Seq[MetadataPair[_]]): MetadataStorage = {
@@ -201,8 +201,8 @@ class MetadataStorageTest extends CompilerTest {
         )
       )
 
-      meta.duplicate shouldNot equal(meta)
-      meta.duplicate shouldNot equal(expected)
+      meta.duplicate shouldEqual meta
+      meta.duplicate shouldEqual expected
     }
 
     "enforce safe construction" in {
diff --git a/engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java b/engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java
index 2d3a856ae3a2..de30c22fbfac 100644
--- a/engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java
+++ b/engine/runtime-parser/src/main/java/org/enso/compiler/core/IR.java
@@ -1,6 +1,5 @@
 package org.enso.compiler.core;
 
-import java.util.Comparator;
 import java.util.UUID;
 import java.util.function.Consumer;
 import java.util.function.Function;
@@ -29,24 +28,6 @@
  * <p>See also: Note [IR Equality and hashing]
  */
 public interface IR {
-  /**
-   * Compares IR structure, but not metadata neither diagnostics. A special comparator used by
-   * <em>Persistance API</em> to perform some rare consistency checks.
-   */
-  public static final Comparator<IR> STRUCTURE_COMPARATOR =
-      (aIr, bIr) -> {
-        if (aIr == bIr) {
-          return 0;
-        }
-        var aCopy = aIr.duplicate(true, false, false, true);
-        var bCopy = bIr.duplicate(true, false, false, true);
-
-        if (aCopy.equals(bCopy)) {
-          return 0;
-        }
-        return System.identityHashCode(aIr) - System.identityHashCode(bIr);
-      };
-
   /**
    * Storage for metadata that the node has been tagged with as the result of various compiler
    * passes.
diff --git a/engine/runtime-parser/src/main/java/org/enso/compiler/core/ir/IrPersistance.java b/engine/runtime-parser/src/main/java/org/enso/compiler/core/ir/IrPersistance.java
index 4dd42faf9462..d317951014c2 100644
--- a/engine/runtime-parser/src/main/java/org/enso/compiler/core/ir/IrPersistance.java
+++ b/engine/runtime-parser/src/main/java/org/enso/compiler/core/ir/IrPersistance.java
@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.util.AbstractList;
 import java.util.ArrayList;
-import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.UUID;
 import org.enso.compiler.core.ir.expression.Application;
@@ -445,33 +444,6 @@ protected Seq readObject(Input in) throws IOException, ClassNotFoundException {
     }
   }
 
-  @ServiceProvider(service = Persistance.class)
-  public static final class PersistMetadataStorage extends Persistance<MetadataStorage> {
-    public PersistMetadataStorage() {
-      super(MetadataStorage.class, false, 389);
-    }
-
-    @Override
-    @SuppressWarnings("unchecked")
-    protected void writeObject(MetadataStorage obj, Output out) throws IOException {
-      var map = new LinkedHashMap<ProcessingPass, ProcessingPass.Metadata>();
-      obj.map(
-          (processingPass, data) -> {
-            map.put(processingPass, data);
-            return null;
-          });
-      out.writeInline(java.util.Map.class, map);
-    }
-
-    @Override
-    @SuppressWarnings("unchecked")
-    protected MetadataStorage readObject(Input in) throws IOException, ClassNotFoundException {
-      var map = in.readInline(java.util.Map.class);
-      var storage = new MetadataStorage(map);
-      return storage;
-    }
-  }
-
   @ServiceProvider(service = Persistance.class)
   public static final class PersistDiagnosticStorage extends Persistance<DiagnosticStorage> {
     public PersistDiagnosticStorage() {
diff --git a/engine/runtime-parser/src/main/java/org/enso/compiler/core/ir/MetadataStorage.java b/engine/runtime-parser/src/main/java/org/enso/compiler/core/ir/MetadataStorage.java
index e0ddd703ae47..4d80ba523ebe 100644
--- a/engine/runtime-parser/src/main/java/org/enso/compiler/core/ir/MetadataStorage.java
+++ b/engine/runtime-parser/src/main/java/org/enso/compiler/core/ir/MetadataStorage.java
@@ -11,18 +11,25 @@
 import java.util.function.BiFunction;
 import java.util.stream.Collectors;
 import org.enso.compiler.core.CompilerStub;
+import org.enso.persist.Persistable;
 import scala.Option;
 
 /** Stores metadata for the various passes. */
+@Persistable(id = 398)
 public final class MetadataStorage {
   private Map<ProcessingPass, ProcessingPass.Metadata> metadata;
 
+  /** Constructs empty, ready to be populated metadata. */
   public MetadataStorage() {
     this(Collections.emptyMap());
   }
 
-  public MetadataStorage(Map<ProcessingPass, ProcessingPass.Metadata> init) {
-    this.metadata = init;
+  MetadataStorage(Map<ProcessingPass, ProcessingPass.Metadata> metaValues) {
+    this.metadata = metaValues;
+  }
+
+  final Map<ProcessingPass, ProcessingPass.Metadata> metaValues() {
+    return this.metadata;
   }
 
   /**
@@ -82,6 +89,15 @@ public Option<ProcessingPass.Metadata> get(ProcessingPass pass) {
     return Option.apply(prev);
   }
 
+  /**
+   * Creates a shallow copy of `this`. Use when re-assigning metadata from one IR to another.
+   *
+   * @return a shallow copy of `this`
+   */
+  public MetadataStorage copy() {
+    return new MetadataStorage(metadata);
+  }
+
   /**
    * Creates a deep copy of `this`.
    *
@@ -214,7 +230,7 @@ public boolean equals(Object obj) {
       return true;
     }
     if (obj instanceof MetadataStorage other) {
-      return this.metadata == other.metadata;
+      return this.metadata.equals(other.metadata);
     }
     return false;
   }
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/CallArgument.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/CallArgument.scala
index a1bc76eb21f2..9d8f14601a0b 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/CallArgument.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/CallArgument.scala
@@ -72,7 +72,7 @@ object CallArgument {
         name != this.name
         || value != this.value
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/DefinitionArgument.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/DefinitionArgument.scala
index 2f34585fa86f..fd820cd62a72 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/DefinitionArgument.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/DefinitionArgument.scala
@@ -123,7 +123,7 @@ object DefinitionArgument {
         || defaultValue != this.defaultValue
         || suspended != this.suspended
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Empty.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Empty.scala
index 698246dd0f93..849d58cd9401 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Empty.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Empty.scala
@@ -35,7 +35,7 @@ sealed case class Empty(
   ): Empty = {
     if (
       location != this.location
-      || passData != this.passData
+      || (passData ne this.passData)
       || diagnostics != this.diagnostics
       || id != this.id
     ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Expression.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Expression.scala
index 2024cb0f24c6..55398add4219 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Expression.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Expression.scala
@@ -90,7 +90,7 @@ object Expression {
         || returnValue != this.returnValue
         || suspended != this.suspended
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -231,7 +231,7 @@ object Expression {
         name != this.name
         || expression != this.expression
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Function.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Function.scala
index 77f47b10968c..021e0c1b57cb 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Function.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Function.scala
@@ -117,7 +117,7 @@ object Function {
         || body != this.body
         || location != this.location
         || canBeTCO != this.canBeTCO
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -283,7 +283,7 @@ object Function {
         || isPrivate != this.isPrivate
         || location != this.location
         || canBeTCO != this.canBeTCO
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Literal.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Literal.scala
index 52d41f2ca739..a5383ca8a336 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Literal.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Literal.scala
@@ -65,7 +65,7 @@ object Literal {
         base != this.base
         || value != this.value
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -197,7 +197,7 @@ object Literal {
       if (
         text != this.text
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala
index 428b054af6d6..b0e95f373572 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Module.scala
@@ -80,7 +80,7 @@ final case class Module(
       || bindings != this.bindings
       || isPrivate != this.isPrivate
       || location != this.location
-      || passData != this.passData
+      || (passData ne this.passData)
       || diagnostics != this.diagnostics
       || id != this.id
     ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Name.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Name.scala
index 8cbd5e328c2b..c4be29a77458 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Name.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Name.scala
@@ -76,7 +76,7 @@ object Name {
         typePointer != this.typePointer
         || methodName != this.methodName
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -246,7 +246,7 @@ object Name {
       if (
         parts != this.parts
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -318,7 +318,7 @@ object Name {
     ): Blank = {
       if (
         location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -400,7 +400,7 @@ object Name {
       if (
         specialName != this.specialName
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -506,7 +506,7 @@ object Name {
         || isMethod != this.isMethod
         || location != this.location
         || originalName != this.originalName
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -616,7 +616,7 @@ object Name {
       if (
         name != this.name
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -711,7 +711,7 @@ object Name {
         name != this.name
         || expression != this.expression
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -822,7 +822,7 @@ object Name {
       if (
         synthetic != this.synthetic
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -921,7 +921,7 @@ object Name {
     ): SelfType = {
       if (
         location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Pattern.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Pattern.scala
index 3343e892c225..7986ff635034 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Pattern.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Pattern.scala
@@ -66,7 +66,7 @@ object Pattern {
       if (
         name != this.name
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -169,7 +169,7 @@ object Pattern {
         constructor != this.constructor
         || fields != this.fields
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -324,7 +324,7 @@ object Pattern {
       if (
         literal != this.literal
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -429,7 +429,7 @@ object Pattern {
         name != this.name
         || tpe != this.tpe
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -549,7 +549,7 @@ object Pattern {
       if (
         doc != this.doc
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Type.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Type.scala
index 1f8590755174..912a6cf848c8 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Type.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/Type.scala
@@ -54,7 +54,7 @@ object Type {
         args != this.args
         || result != this.result
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -171,7 +171,7 @@ object Type {
         || signature != this.signature
         || comment != this.comment
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -287,7 +287,7 @@ object Type {
         typed != this.typed
         || context != this.context
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -399,7 +399,7 @@ object Type {
         typed != this.typed
         || error != this.error
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Application.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Application.scala
index b13add81995c..1778b046c156 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Application.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Application.scala
@@ -86,7 +86,7 @@ object Application {
         || arguments != this.arguments
         || hasDefaultsSuspended != this.hasDefaultsSuspended
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -203,7 +203,7 @@ object Application {
       if (
         target != this.target
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -327,7 +327,7 @@ object Application {
       if (
         expression != this.expression
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -430,7 +430,7 @@ object Application {
       if (
         items != this.items
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Case.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Case.scala
index 244f7344f1d7..62b74e3f6e34 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Case.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Case.scala
@@ -73,7 +73,7 @@ object Case {
         || branches != this.branches
         || isNested != this.isNested
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -200,7 +200,7 @@ object Case {
         || expression != this.expression
         || terminalBranch != this.terminalBranch
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Comment.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Comment.scala
index af7bc15bab5b..aec36d55ac0e 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Comment.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Comment.scala
@@ -62,7 +62,7 @@ object Comment {
       if (
         doc != this.doc
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Error.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Error.scala
index d298bce2a919..61cf402259ee 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Error.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Error.scala
@@ -63,7 +63,7 @@ object Error {
     ): InvalidIR = {
       if (
         ir != this.ir
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Foreign.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Foreign.scala
index bbc88899bb28..0b5bbf151237 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Foreign.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Foreign.scala
@@ -70,7 +70,7 @@ object Foreign {
         lang != this.lang
         || code != this.code
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Operator.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Operator.scala
index 3a5027b7c05f..a9766a023e3f 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Operator.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Operator.scala
@@ -72,7 +72,7 @@ object Operator {
         || operator != this.operator
         || right != this.right
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Section.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Section.scala
index 1ab580d5c3c3..0e84be2aa3c6 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Section.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/Section.scala
@@ -67,7 +67,7 @@ object Section {
         arg != this.arg
         || operator != this.operator
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -174,7 +174,7 @@ object Section {
       if (
         operator != this.operator
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -277,7 +277,7 @@ object Section {
         operator != this.operator
         || arg != this.arg
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Conversion.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Conversion.scala
index 276612dcf43b..d58369499372 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Conversion.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Conversion.scala
@@ -55,7 +55,7 @@ sealed case class Conversion(
     if (
       storedIr != this.storedIr
       || reason != this.reason
-      || passData != this.passData
+      || (passData ne this.passData)
       || diagnostics != this.diagnostics
       || id != this.id
     ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/ImportExport.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/ImportExport.scala
index 64f7c6d359bf..fb9c3ef98ed4 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/ImportExport.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/ImportExport.scala
@@ -62,7 +62,7 @@ sealed case class ImportExport(
     if (
       ir != this.ir
       || reason != this.reason
-      || passData != this.passData
+      || (passData ne this.passData)
       || diagnostics != this.diagnostics
       || id != this.id
     ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Pattern.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Pattern.scala
index 172c047e9823..2305cbe4bcaa 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Pattern.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Pattern.scala
@@ -67,7 +67,7 @@ sealed case class Pattern(
     if (
       originalPattern != this.originalPattern
       || reason != this.reason
-      || passData != this.passData
+      || (passData ne this.passData)
       || diagnostics != this.diagnostics
       || id != this.id
     ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Redefined.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Redefined.scala
index e375d7e1e179..69627bda0192 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Redefined.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Redefined.scala
@@ -66,7 +66,7 @@ object Redefined {
     ): SelfArg = {
       if (
         location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -161,7 +161,7 @@ object Redefined {
         targetType != this.targetType
         || sourceType != this.sourceType
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -291,7 +291,7 @@ object Redefined {
         typeName != this.typeName
         || methodName != this.methodName
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -421,7 +421,7 @@ object Redefined {
         atomName != this.atomName
         || methodName != this.methodName
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -544,7 +544,7 @@ object Redefined {
       if (
         typeName != this.typeName
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -650,7 +650,7 @@ object Redefined {
       if (
         name != this.name
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -751,7 +751,7 @@ object Redefined {
     ): Binding = {
       if (
         invalidBinding != this.invalidBinding
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Resolution.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Resolution.scala
index 269e241d2ecb..21c8d5c2f02f 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Resolution.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Resolution.scala
@@ -71,7 +71,7 @@ sealed case class Resolution(
     if (
       originalName != this.originalName
       || reason != this.reason
-      || passData != this.passData
+      || (passData ne this.passData)
       || diagnostics != this.diagnostics
       || id != this.id
     ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Syntax.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Syntax.scala
index a61fd2f53bc5..5398a563aaf5 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Syntax.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Syntax.scala
@@ -63,7 +63,7 @@ sealed case class Syntax(
     if (
       at != this.at
       || reason != this.reason
-      || passData != this.passData
+      || (passData ne this.passData)
       || diagnostics != this.diagnostics
       || id != this.id
     ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Unexpected.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Unexpected.scala
index 7b3a5a2e3db2..655db3f4ad23 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Unexpected.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/expression/errors/Unexpected.scala
@@ -77,7 +77,7 @@ object Unexpected {
     ): TypeSignature = {
       if (
         ir != this.ir
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Definition.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Definition.scala
index 1eb7ed786660..df289a370d64 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Definition.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Definition.scala
@@ -78,7 +78,7 @@ object Definition {
         || params != this.params
         || members != this.members
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -206,7 +206,7 @@ object Definition {
         || annotations != this.annotations
         || isPrivate != this.isPrivate
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -338,7 +338,7 @@ object Definition {
         || arguments != this.arguments
         || body != this.body
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Export.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Export.scala
index aa289ba8ecb5..a845e03c426c 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Export.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Export.scala
@@ -88,7 +88,7 @@ object Export {
         || onlyNames != this.onlyNames
         || isSynthetic != this.isSynthetic
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Import.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Import.scala
index 754ee568a74a..da8ca4f59345 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Import.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/Import.scala
@@ -97,7 +97,7 @@ object Import {
         || hiddenNames != this.hiddenNames
         || isSynthetic != this.isSynthetic
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/definition/Method.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/definition/Method.scala
index 20a4feeab662..ecb23c8d42c7 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/definition/Method.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/definition/Method.scala
@@ -115,7 +115,7 @@ object Method {
         || isPrivate != this.isPrivate
         || isStaticWrapperForInstanceMethod != this.isStaticWrapperForInstanceMethod
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -321,7 +321,7 @@ object Method {
         || isPrivate != this.isPrivate
         || body != this.body
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -493,7 +493,7 @@ object Method {
         || sourceTypeName != this.sourceTypeName
         || body != this.body
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/imports/Polyglot.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/imports/Polyglot.scala
index 4a7484eaa0a7..3826e30d2e6c 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/imports/Polyglot.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/module/scope/imports/Polyglot.scala
@@ -55,7 +55,7 @@ sealed case class Polyglot(
       entity != this.entity
       || rename != this.rename
       || location != this.location
-      || passData != this.passData
+      || (passData ne this.passData)
       || diagnostics != this.diagnostics
       || id != this.id
     ) {
diff --git a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/type/Set.scala b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/type/Set.scala
index d40e3cf37dc7..2f3ffabf8327 100644
--- a/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/type/Set.scala
+++ b/engine/runtime-parser/src/main/scala/org/enso/compiler/core/ir/type/Set.scala
@@ -74,7 +74,7 @@ object Set {
         || memberType != this.memberType
         || value != this.value
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -202,7 +202,7 @@ object Set {
         left != this.left
         || right != this.right
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -315,7 +315,7 @@ object Set {
         left != this.left
         || right != this.right
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -428,7 +428,7 @@ object Set {
         left != this.left
         || right != this.right
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -535,7 +535,7 @@ object Set {
       if (
         operands != this.operands
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
@@ -642,7 +642,7 @@ object Set {
         left != this.left
         || right != this.right
         || location != this.location
-        || passData != this.passData
+        || (passData ne this.passData)
         || diagnostics != this.diagnostics
         || id != this.id
       ) {
diff --git a/engine/runtime-parser/src/test/java/org/enso/compiler/core/IrPersistanceTest.java b/engine/runtime-parser/src/test/java/org/enso/compiler/core/IrPersistanceTest.java
index 1ee473a58de8..81b69719101c 100644
--- a/engine/runtime-parser/src/test/java/org/enso/compiler/core/IrPersistanceTest.java
+++ b/engine/runtime-parser/src/test/java/org/enso/compiler/core/IrPersistanceTest.java
@@ -419,9 +419,9 @@ public void nameLiteral() throws Exception {
     var loc = new IdentifiedLocation(new Location(5, 19), null);
     var in = new Name.Literal("anyName", true, loc, Option.empty(), new MetadataStorage());
 
-    var out = serde(Name.Literal.class, in, 39);
-    assertEquals("They are structurally equal", 0, IR.STRUCTURE_COMPARATOR.compare(in, out));
-    assertNotEquals("But not .equals (currently)", in, out);
+    var out = serde(Name.Literal.class, in, -1);
+    assertEquals("They are structurally equal", in, out);
+    assertNotSame("But not ==", in, out);
   }
 
   private static <T> T serde(Class<T> clazz, T l, int expectedSize) throws IOException {
diff --git a/lib/java/persistance/src/main/java/org/enso/persist/PerInputImpl.java b/lib/java/persistance/src/main/java/org/enso/persist/PerInputImpl.java
index 2df0d6113973..5785cfd65dd6 100644
--- a/lib/java/persistance/src/main/java/org/enso/persist/PerInputImpl.java
+++ b/lib/java/persistance/src/main/java/org/enso/persist/PerInputImpl.java
@@ -7,7 +7,6 @@
 import java.io.DataInputStream;
 import java.io.IOException;
 import java.nio.ByteBuffer;
-import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Objects;
@@ -237,27 +236,9 @@ static Object readIndirect(InputCache cache, PerMap map, Input in) throws IOExce
     return res;
   }
 
-  private static Class<?> irClass;
-  private static Comparator STRUCTURE_COMPARATOR;
-
   @SuppressWarnings("unchecked")
   private static boolean gentlyEquals(Object o1, Object o2) {
-    if (Objects.equals(o1, o2)) {
-      return true;
-    }
-    try {
-      if (STRUCTURE_COMPARATOR == null) {
-        irClass = Class.forName("org.enso.compiler.core.IR");
-        var comparatorField = irClass.getField("STRUCTURE_COMPARATOR");
-        STRUCTURE_COMPARATOR = (java.util.Comparator) comparatorField.get(null);
-      }
-      if (irClass.isInstance(o1) && irClass.isInstance(o2)) {
-        return STRUCTURE_COMPARATOR.compare(o1, o2) == 0;
-      }
-    } catch (ReflectiveOperationException ex) {
-      PerUtils.LOG.warn("Cannot compare " + o1.getClass(), ex);
-    }
-    return false;
+    return Objects.equals(o1, o2);
   }
 
   private static void dumpObject(StringBuilder sb, Object obj) {