diff --git a/src/org/sosy_lab/common/configuration/Configuration.java b/src/org/sosy_lab/common/configuration/Configuration.java
index d8e935c7e..beda3382f 100644
--- a/src/org/sosy_lab/common/configuration/Configuration.java
+++ b/src/org/sosy_lab/common/configuration/Configuration.java
@@ -91,6 +91,8 @@ public final class Configuration {
 
   private static boolean secureMode = false;
 
+  private final Configuration parent;
+
   /** Create a new Builder instance. */
   public static ConfigurationBuilder builder() {
     return new ConfigurationBuilder();
@@ -116,6 +118,7 @@ public static Configuration defaultConfiguration() {
         new HashSet<>(0),
         new HashSet<>(0),
         null,
+        null,
         null);
   }
 
@@ -131,7 +134,8 @@ public static Configuration copyWithNewPrefix(Configuration oldConfig, String ne
         oldConfig.unusedProperties,
         oldConfig.deprecatedProperties,
         oldConfig.printUsedOptions,
-        oldConfig.logger);
+        oldConfig.logger,
+        oldConfig);
   }
 
   /** Splitter to create string arrays. */
@@ -291,7 +295,8 @@ LogManager getLogger() {
       Set<String> pUnusedProperties,
       Set<String> pDeprecatedProperties,
       @Nullable PrintStream pPrintUsedOptions,
-      @Nullable LogManager pLogger) {
+      @Nullable LogManager pLogger,
+      @Nullable Configuration pParent) {
 
     checkNotNull(pProperties);
     checkNotNull(pSources);
@@ -306,6 +311,7 @@ LogManager getLogger() {
     deprecatedProperties = checkNotNull(pDeprecatedProperties);
     printUsedOptions = pPrintUsedOptions;
     logger = firstNonNull(pLogger, LogManager.createNullLogManager());
+    parent = pParent;
   }
 
   public void enableLogging(LogManager pLogger) {
@@ -335,10 +341,16 @@ public String getProperty(String key) {
     checkNotNull(key);
     @Var String result = properties.get(prefix + key);
     unusedProperties.remove(prefix + key);
+    if (parent != null && result != null && result.equals(parent.getProperty(prefix + key))) {
+        parent.unusedProperties.remove(prefix + key);
+    }
 
     if (result == null && !prefix.isEmpty()) {
       result = properties.get(key);
       unusedProperties.remove(key);
+      if (parent != null && result != null && result.equals(parent.getProperty(key))) {
+        parent.unusedProperties.remove(key);
+      }
     }
     return result;
   }
diff --git a/src/org/sosy_lab/common/configuration/ConfigurationBuilder.java b/src/org/sosy_lab/common/configuration/ConfigurationBuilder.java
index d6f5033f8..6bde7a284 100644
--- a/src/org/sosy_lab/common/configuration/ConfigurationBuilder.java
+++ b/src/org/sosy_lab/common/configuration/ConfigurationBuilder.java
@@ -24,6 +24,7 @@
 import static com.google.common.base.Preconditions.checkState;
 
 import com.google.common.collect.ImmutableMap;
+import com.google.common.collect.Sets;
 import com.google.common.io.CharSource;
 import com.google.common.io.Resources;
 import com.google.errorprone.annotations.CanIgnoreReturnValue;
@@ -122,8 +123,10 @@ public ConfigurationBuilder setPrefix(String newPrefix) {
 
   /**
    * Copy everything from an existing Configuration instance. This also means that the new
-   * configuration object created by this builder will share the set of unused properties with the
-   * configuration instance passed to this class.
+   * configuration object created by this builder will update the set of unused properties of the
+   * configuration instance passed to this class in case a property is requested. The new
+   * configuration will keep track of unused properties only for properties that are not present in
+   * the passed instance.
    *
    * <p>If this method is called, it has to be the first method call on this builder instance.
    *
@@ -374,7 +377,8 @@ public Configuration build() throws InvalidConfigurationException {
     Set<String> newDeprecatedProperties;
     if (oldConfig != null) {
       // share the same set of unused properties
-      newUnusedProperties = oldConfig.unusedProperties;
+      newUnusedProperties =
+          new HashSet<>(Sets.difference(newProperties.keySet(), oldConfig.properties.keySet()));
       newDeprecatedProperties = oldConfig.deprecatedProperties;
     } else {
       newUnusedProperties = new HashSet<>(newProperties.keySet());
@@ -394,7 +398,8 @@ public Configuration build() throws InvalidConfigurationException {
             newUnusedProperties,
             newDeprecatedProperties,
             oldConfig != null ? oldConfig.getUsedOptionsPrintStream() : null,
-            oldConfig != null ? oldConfig.getLogger() : null);
+            oldConfig != null ? oldConfig.getLogger() : null,
+            oldConfig);
 
     // reset builder instance so that it may be re-used
     properties = null;
@@ -432,7 +437,8 @@ private ImmutableMap<Class<?>, TypeConverter> buildNewConverters(
             newUnusedProperties,
             newDeprecatedProperties,
             oldConfig != null ? oldConfig.getUsedOptionsPrintStream() : null,
-            oldConfig != null ? oldConfig.getLogger() : null);
+            oldConfig != null ? oldConfig.getLogger() : null,
+            oldConfig);
 
     // This map serves as a cache: if a single TypeConverter is used for multiple types,
     // we call getInstanceForNewConfiguration only once and use the new instance several times.