diff --git a/wres-config/src/wres/config/yaml/DeclarationUtilities.java b/wres-config/src/wres/config/yaml/DeclarationUtilities.java
index 1f0d9b031..994220a80 100644
--- a/wres-config/src/wres/config/yaml/DeclarationUtilities.java
+++ b/wres-config/src/wres/config/yaml/DeclarationUtilities.java
@@ -891,22 +891,26 @@ public static EvaluationDeclaration removeFeaturesWithoutThresholds( EvaluationD
 
         Set<Threshold> thresholds = DeclarationUtilities.getInbandThresholds( declaration );
 
-        // Get the names of features with thresholds
+        // Get the names of features with thresholds that were read from a source and not generated by the software:
+        // see GitHub #429
         Set<String> leftFeatureNamesWithThresholds = thresholds.stream()
                                                                .filter( n -> n.featureNameFrom()
-                                                                             == DatasetOrientation.LEFT )
+                                                                             == DatasetOrientation.LEFT
+                                                                             && !n.generated() )
                                                                .map( n -> n.feature()
                                                                            .getName() )
                                                                .collect( Collectors.toSet() );
         Set<String> rightFeatureNamesWithThresholds = thresholds.stream()
                                                                 .filter( n -> n.featureNameFrom()
-                                                                              == DatasetOrientation.RIGHT )
+                                                                              == DatasetOrientation.RIGHT
+                                                                              && !n.generated() )
                                                                 .map( n -> n.feature()
                                                                             .getName() )
                                                                 .collect( Collectors.toSet() );
         Set<String> baselineFeatureNamesWithThresholds = thresholds.stream()
                                                                    .filter( n -> n.featureNameFrom()
-                                                                                 == DatasetOrientation.BASELINE )
+                                                                                 == DatasetOrientation.BASELINE
+                                                                                 && !n.generated() )
                                                                    .map( n -> n.feature()
                                                                                .getName() )
                                                                    .collect( Collectors.toSet() );
diff --git a/wres-config/test/wres/config/yaml/DeclarationUtilitiesTest.java b/wres-config/test/wres/config/yaml/DeclarationUtilitiesTest.java
index cb51255e6..199460f74 100644
--- a/wres-config/test/wres/config/yaml/DeclarationUtilitiesTest.java
+++ b/wres-config/test/wres/config/yaml/DeclarationUtilitiesTest.java
@@ -776,7 +776,7 @@ void testIsReadableFileReturnsFalseForInvalidPath()
                   - some_file.csv
                 predicted:
                   - another_file.csv
-                  """;
+                """;
 
         FileSystem fileSystem = FileSystems.getDefault();
         assertFalse( DeclarationUtilities.isReadableFile( fileSystem, path ) );
@@ -1184,6 +1184,9 @@ void testRemoveFeaturesWithoutThresholds()
         Geometry baseline = Geometry.newBuilder()
                                     .setName( "baz" )
                                     .build();
+        Geometry allDataGeometry = Geometry.newBuilder()
+                                           .setName( "qux" )
+                                           .build();
 
         // Tuple foo-bar-baz
         GeometryTuple one = GeometryTuple.newBuilder()
@@ -1204,6 +1207,13 @@ void testRemoveFeaturesWithoutThresholds()
                                            .setBaseline( left )
                                            .build();
 
+        // Tuple qux
+        GeometryTuple four = GeometryTuple.newBuilder()
+                                          .setLeft( allDataGeometry )
+                                          .setRight( allDataGeometry )
+                                          .setBaseline( allDataGeometry )
+                                          .build();
+
         Threshold threshold = Threshold.newBuilder()
                                        .setLeftThresholdValue( 1 )
                                        .build();
@@ -1225,8 +1235,12 @@ void testRemoveFeaturesWithoutThresholds()
                                 .feature( baseline )
                                 .featureNameFrom( DatasetOrientation.BASELINE )
                                 .build();
+        wres.config.yaml.components.Threshold allDataThreshold =
+                ThresholdBuilder.builder( DeclarationUtilities.GENERATED_ALL_DATA_THRESHOLD )
+                                .feature( allDataGeometry )
+                                .build();
 
-        Set<GeometryTuple> geometryTuples = Set.of( one, two, three );
+        Set<GeometryTuple> geometryTuples = Set.of( one, two, three, four );
         Features features = FeaturesBuilder.builder()
                                            .geometries( geometryTuples )
                                            .build();
@@ -1243,7 +1257,8 @@ void testRemoveFeaturesWithoutThresholds()
                                             .featureGroups( featureGroups )
                                             .thresholds( Set.of( wrappedThresholdOne,
                                                                  wrappedThresholdTwo,
-                                                                 wrappedThresholdThree ) )
+                                                                 wrappedThresholdThree,
+                                                                 allDataThreshold ) )
                                             .build();
 
         EvaluationDeclaration actual = DeclarationUtilities.removeFeaturesWithoutThresholds( declaration );
@@ -1263,7 +1278,8 @@ void testRemoveFeaturesWithoutThresholds()
                                                                      .featureGroups( expectedFeatureGroups )
                                                                      .thresholds( Set.of( wrappedThresholdOne,
                                                                                           wrappedThresholdTwo,
-                                                                                          wrappedThresholdThree ) )
+                                                                                          wrappedThresholdThree,
+                                                                                          allDataThreshold ) )
                                                                      .build();
 
         assertEquals( expected, actual );
@@ -1274,11 +1290,11 @@ void testRemoveFeaturesWithoutThresholdsRemovesNoFeaturesWhenEachFeatureHasAThre
     {
         // Tests GitHub issue #319
         Geometry oneObserved = Geometry.newBuilder()
-                                .setName( "one_observed" )
-                                .build();
+                                       .setName( "one_observed" )
+                                       .build();
         Geometry onePredicted = Geometry.newBuilder()
-                                 .setName( "one_predicted" )
-                                 .build();
+                                        .setName( "one_predicted" )
+                                        .build();
         Geometry twoObserved = Geometry.newBuilder()
                                        .setName( "two_observed" )
                                        .build();
diff --git a/wres-reading/src/wres/reading/wrds/thresholds/WrdsThresholdReader.java b/wres-reading/src/wres/reading/wrds/thresholds/WrdsThresholdReader.java
index 92a0ea4a5..44afc769e 100644
--- a/wres-reading/src/wres/reading/wrds/thresholds/WrdsThresholdReader.java
+++ b/wres-reading/src/wres/reading/wrds/thresholds/WrdsThresholdReader.java
@@ -704,7 +704,8 @@ private static void validate( URI uri,
         Set<String> thresholdNamesWithoutFeatures = new TreeSet<>( thresholdFeatureNames );
         thresholdNamesWithoutFeatures.removeAll( featureNames.keySet() );
 
-        if ( ( !featureNamesWithoutThresholds.isEmpty() || !thresholdNamesWithoutFeatures.isEmpty() )
+        if ( ( !featureNamesWithoutThresholds.isEmpty()
+               || !thresholdNamesWithoutFeatures.isEmpty() )
              && LOGGER.isWarnEnabled() )
         {
             LOGGER.warn( "{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}{}",