diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/crossreference/UndirectedCrossReferenceInitializer.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/crossreference/UndirectedCrossReferenceInitializer.java
index d0784c272..449db5f20 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/crossreference/UndirectedCrossReferenceInitializer.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/crossreference/UndirectedCrossReferenceInitializer.java
@@ -15,7 +15,9 @@
 import tools.refinery.store.representation.Symbol;
 import tools.refinery.store.tuple.Tuple;
 
+import java.util.HashSet;
 import java.util.LinkedHashMap;
+import java.util.Set;
 
 class UndirectedCrossReferenceInitializer implements PartialModelInitializer {
 	private final PartialRelation linkType;
@@ -30,11 +32,23 @@ class UndirectedCrossReferenceInitializer implements PartialModelInitializer {
 	public void initialize(Model model, ModelSeed modelSeed) {
 		var mergedMap = getMergedMap(modelSeed);
 		var interpretation = model.getInterpretation(symbol);
+
+		var oldCursor = interpretation.getAll();
+		Set<Tuple> oldKeys = new HashSet<>();
+		while (oldCursor.move()) {
+			oldKeys.add(oldCursor.getKey());
+		}
+
 		for (var entry : mergedMap.entrySet()) {
 			var key = entry.getKey();
 			var value = entry.getValue();
+			oldKeys.remove(key);
 			interpretation.put(key, value);
 		}
+
+		for (var unusedOldKey : oldKeys) {
+			interpretation.put(unusedOldKey, symbol.defaultValue());
+		}
 	}
 
 	@NotNull
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/MultiObjectInitializer.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/MultiObjectInitializer.java
index 955dc1f47..3ed9db27b 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/MultiObjectInitializer.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/multiobject/MultiObjectInitializer.java
@@ -6,6 +6,7 @@
 package tools.refinery.store.reasoning.translator.multiobject;
 
 import org.jetbrains.annotations.NotNull;
+import tools.refinery.store.model.Interpretation;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.reasoning.ReasoningAdapter;
 import tools.refinery.store.reasoning.refinement.PartialModelInitializer;
@@ -17,8 +18,10 @@
 import tools.refinery.logic.term.cardinalityinterval.CardinalityIntervals;
 import tools.refinery.store.tuple.Tuple;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.List;
 import java.util.function.Function;
 
 class MultiObjectInitializer implements PartialModelInitializer {
@@ -30,10 +33,13 @@ public MultiObjectInitializer(Symbol<CardinalityInterval> countSymbol) {
 
 	@Override
 	public void initialize(Model model, ModelSeed modelSeed) {
+		var countInterpretation = model.getInterpretation(countSymbol);
+		eraseNodeCardinalityOverLimit(countInterpretation, modelSeed.getNodeCount());
+
 		var intervals = initializeIntervals(model, modelSeed);
 		initializeExists(intervals, model, modelSeed);
 		initializeEquals(intervals, model, modelSeed);
-		var countInterpretation = model.getInterpretation(countSymbol);
+
 		var uniqueTable = new HashMap<CardinalityInterval, CardinalityInterval>();
 		for (int i = 0; i < intervals.length; i++) {
 			var uniqueInterval = uniqueTable.computeIfAbsent(intervals[i], Function.identity());
@@ -41,6 +47,21 @@ public void initialize(Model model, ModelSeed modelSeed) {
 		}
 	}
 
+	private void eraseNodeCardinalityOverLimit(Interpretation<CardinalityInterval> interpretation, int limit) {
+		var cursor = interpretation.getAll();
+		List<Integer> toDelete = new ArrayList<>();
+		while(cursor.move()) {
+			int index = cursor.getKey().get(0);
+			if(index >= limit) {
+				toDelete.add(index);
+			}
+		}
+		for(var index : toDelete) {
+			interpretation.put(Tuple.of(index), countSymbol.defaultValue());
+		}
+	}
+
+
 	@NotNull
 	private CardinalityInterval[] initializeIntervals(Model model, ModelSeed modelSeed) {
 		var intervals = new CardinalityInterval[modelSeed.getNodeCount()];
@@ -126,4 +147,5 @@ private void checkNodeId(CardinalityInterval[] intervals, int nodeId) {
 					.formatted(nodeId, intervals.length));
 		}
 	}
+
 }
diff --git a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeHierarchyInitializer.java b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeHierarchyInitializer.java
index aa76d927f..15ee95458 100644
--- a/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeHierarchyInitializer.java
+++ b/subprojects/store-reasoning/src/main/java/tools/refinery/store/reasoning/translator/typehierarchy/TypeHierarchyInitializer.java
@@ -5,6 +5,7 @@
  */
 package tools.refinery.store.reasoning.translator.typehierarchy;
 
+import tools.refinery.store.model.Interpretation;
 import tools.refinery.store.model.Model;
 import tools.refinery.store.reasoning.refinement.PartialModelInitializer;
 import tools.refinery.store.reasoning.representation.PartialRelation;
@@ -13,8 +14,10 @@
 import tools.refinery.logic.term.truthvalue.TruthValue;
 import tools.refinery.store.tuple.Tuple;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.List;
 import java.util.function.Function;
 
 public class TypeHierarchyInitializer implements PartialModelInitializer {
@@ -28,13 +31,16 @@ public TypeHierarchyInitializer(TypeHierarchy typeHierarchy, Symbol<InferredType
 
 	@Override
 	public void initialize(Model model, ModelSeed modelSeed) {
+		var typeInterpretation = model.getInterpretation(typeSymbol);
+		eraseNodeTypesOverLimit(typeInterpretation, modelSeed.getNodeCount());
+
 		var inferredTypes = new InferredType[modelSeed.getNodeCount()];
 		Arrays.fill(inferredTypes, typeHierarchy.getUnknownType());
 		for (var type : typeHierarchy.getAllTypes()) {
 			model.checkCancelled();
 			initializeType(type, inferredTypes, model, modelSeed);
 		}
-		var typeInterpretation = model.getInterpretation(typeSymbol);
+
 		var uniqueTable = new HashMap<InferredType, InferredType>();
 		for (int i = 0; i < inferredTypes.length; i++) {
 			model.checkCancelled();
@@ -43,6 +49,20 @@ public void initialize(Model model, ModelSeed modelSeed) {
 		}
 	}
 
+	private void eraseNodeTypesOverLimit(Interpretation<InferredType> interpretation, int limit) {
+		var cursor = interpretation.getAll();
+		List<Integer> toDelete = new ArrayList<>();
+		while(cursor.move()) {
+			int index = cursor.getKey().get(0);
+			if(index >= limit) {
+				toDelete.add(index);
+			}
+		}
+		for(var index : toDelete) {
+			interpretation.put(Tuple.of(index), typeSymbol.defaultValue());
+		}
+	}
+
 	private void initializeType(PartialRelation type, InferredType[] inferredTypes, Model model, ModelSeed modelSeed) {
 		var cursor = modelSeed.getCursor(type, TruthValue.UNKNOWN);
 		var analysisResult = typeHierarchy.getAnalysisResult(type);