diff --git a/plugins/catalog-backend/src/database/DefaultProcessingDatabase.test.ts b/plugins/catalog-backend/src/database/DefaultProcessingDatabase.test.ts
index 4fbb38b4fc..540c93ef13 100644
--- a/plugins/catalog-backend/src/database/DefaultProcessingDatabase.test.ts
+++ b/plugins/catalog-backend/src/database/DefaultProcessingDatabase.test.ts
@@ -462,12 +462,17 @@ describe('DefaultProcessingDatabase', () => {
               knexTx<DbRefreshStateReferencesRow>(
                 'refresh_state_references',
               ).select(),
-            ).resolves.toEqual([
-              expect.objectContaining({
-                source_entity_ref: 'location:default/fakelocation',
-                target_entity_ref: 'component:default/1',
-              }),
-            ]);
+            ).resolves.toEqual(
+              step.expectConflict
+                ? []
+                : [
+                    // eslint-disable-next-line jest/no-conditional-expect
+                    expect.objectContaining({
+                      source_entity_ref: 'location:default/fakelocation',
+                      target_entity_ref: 'component:default/1',
+                    }),
+                  ],
+            );
 
             expect(mockLogger.error).not.toHaveBeenCalled();
           }
diff --git a/plugins/catalog-backend/src/database/DefaultProcessingDatabase.ts b/plugins/catalog-backend/src/database/DefaultProcessingDatabase.ts
index 1127deed7e..761f5bfd72 100644
--- a/plugins/catalog-backend/src/database/DefaultProcessingDatabase.ts
+++ b/plugins/catalog-backend/src/database/DefaultProcessingDatabase.ts
@@ -314,7 +314,6 @@ export class DefaultProcessingDatabase implements ProcessingDatabase {
 
     // Keeps track of the entities that we end up inserting to update refresh_state_references afterwards
     const stateReferences = new Array<string>();
-    const conflictingStateReferences = new Array<string>();
 
     // Upsert all of the unprocessed entities into the refresh_state table, by
     // their entity ref.
@@ -357,13 +356,11 @@ export class DefaultProcessingDatabase implements ProcessingDatabase {
         this.options.logger.warn(
           `Detected conflicting entityRef ${entityRef} already referenced by ${conflictingKey} and now also ${locationKey}`,
         );
-        conflictingStateReferences.push(entityRef);
       }
     }
 
     // Replace all references for the originating entity or source and then create new ones
     await tx<DbRefreshStateReferencesRow>('refresh_state_references')
-      .whereNotIn('target_entity_ref', conflictingStateReferences)
       .andWhere({ source_entity_ref: options.sourceEntityRef })
       .delete();
     await tx.batchInsert(
diff --git a/plugins/catalog-backend/src/database/DefaultProviderDatabase.ts b/plugins/catalog-backend/src/database/DefaultProviderDatabase.ts
index f1073fd984..a0d376327b 100644
--- a/plugins/catalog-backend/src/database/DefaultProviderDatabase.ts
+++ b/plugins/catalog-backend/src/database/DefaultProviderDatabase.ts
@@ -161,6 +161,11 @@ export class DefaultProviderDatabase implements ProviderDatabase {
             });
           }
 
+          await tx<DbRefreshStateReferencesRow>('refresh_state_references')
+            .where('target_entity_ref', entityRef)
+            .andWhere({ source_key: options.sourceKey })
+            .delete();
+
           if (ok) {
             await tx<DbRefreshStateReferencesRow>(
               'refresh_state_references',