diff --git a/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/MigrationService.java b/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/MigrationService.java
index b0f05859e33a85bc285a05056d5c16448a4cb4f0..9786e3974752bb0e9281d42a3ef92fa1bab8c5c2 100644
--- a/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/MigrationService.java
+++ b/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/MigrationService.java
@@ -28,7 +28,6 @@ import java.util.Map.Entry;
 import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.emf.common.util.BasicEList;
 import org.eclipse.emf.ecore.EObject;
-import org.eclipse.emf.ecore.util.EcoreUtil;
 import org.eclipse.emf.ecore.util.FeatureMap;
 import org.eclipse.emf.ecore.xml.type.AnyType;
 import org.fortiss.tooling.kernel.ToolingKernelActivator;
@@ -138,10 +137,7 @@ public class MigrationService extends ObjectAwareServiceBase<IMigrationProvider>
 					error(ToolingKernelActivator.getDefault(), input.getSaveableName() +
 							" contains one or more unknown feature(s) which will be deleted: " +
 							featuresToStrings(unknownFeatures));
-
-					for(Entry<EObject, AnyType> e : unknownFeatures.entrySet()) {
-						EcoreUtil.delete(e.getKey(), true);
-					}
+					unknownFeatures.clear();
 				}
 			}
 		});
diff --git a/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/storage/eclipse/.ratings b/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/storage/eclipse/.ratings
index 4a4edee0b9b29c4f7e79c5026854886346e3d02a..129d11bd34f93177884c7de7a03710e9bb2c8298 100644
--- a/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/storage/eclipse/.ratings
+++ b/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/storage/eclipse/.ratings
@@ -1,5 +1,5 @@
 AutoUndoCommandStack.java fc326adf66c6cea2354884cdc240da5f2f82689a GREEN
 EMFTransactionalCommand.java ba4b5bead9768b6ce6c955b9238cd96cb722533c GREEN
 EclipseResourceStorageService.java e29e32272286921c5e43963253902b3ba54490c7 GREEN
-ModelContext.java 55de5f19c5d625f935fb8136ff72d80b3a54ff19 GREEN
+ModelContext.java db1735834c85e7b508266f56463d011f2b72af0e YELLOW
 NonDirtyingEMFTransactionalCommand.java d288ebe35d22442c603496b0c917fb99a8febeea GREEN
diff --git a/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/storage/eclipse/ModelContext.java b/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/storage/eclipse/ModelContext.java
index 55de5f19c5d625f935fb8136ff72d80b3a54ff19..db1735834c85e7b508266f56463d011f2b72af0e 100644
--- a/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/storage/eclipse/ModelContext.java
+++ b/org.fortiss.tooling.kernel/src/org/fortiss/tooling/kernel/internal/storage/eclipse/ModelContext.java
@@ -330,7 +330,9 @@ class ModelContext implements ITopLevelElement, CommandStackListener {
 
 		// Step 3..n: Save resources not managed by kernel
 		for(Resource currentResource : rset.getResources()) {
-			if(currentResource != resource && !editingDomain.isReadOnly(currentResource)) {
+			if(currentResource != resource && !editingDomain.isReadOnly(currentResource) &&
+					!currentResource.getContents().isEmpty()) {
+				// do not save resources which are not contained (by a FileProject)
 				try {
 					currentResource.save(saveOptions);
 				} catch(IOException e) {