diff --git a/src/main/components/store/merge.ts b/src/main/components/store/merge.ts
new file mode 100644
index 00000000..11a8b2c7
--- /dev/null
+++ b/src/main/components/store/merge.ts
@@ -0,0 +1,44 @@
+import { ModelState } from '../../components/store/model-state';
+import { AssessmentState } from '../../services/assessment/assessment-types';
+import { UMLElementState } from '../../services/uml-element/uml-element-types';
+
+/**
+ * Merges the old state with the new state. In particular, it maintains
+ * all potential prototypes, and gracefully updates owned elements list in the
+ * diagram. The boundaries of the diagram are NOT updated, which is to be done, if
+ * necessary, by some subsequent side-effect.
+ * @param oldState
+ * @param newState
+ * @returns The merged state.
+ */
+export function merge(oldState: ModelState, newState: ModelState): ModelState {
+  return {
+    ...oldState,
+    diagram: {
+      ...oldState.diagram,
+      ownedElements: oldState.diagram.ownedElements.filter(
+        (id) => !!newState.elements[id] && !newState.elements[id].owner,
+      ),
+      ownedRelationships: oldState.diagram.ownedRelationships.filter((id) => !!newState.elements[id]),
+    },
+    elements: Object.keys(newState.elements).reduce((acc, id) => {
+      return {
+        ...acc,
+        [id]: {
+          ...oldState.elements[id],
+          ...newState.elements[id],
+        },
+      };
+    }, {} as UMLElementState),
+    interactive: newState.interactive,
+    assessments: Object.keys(newState.assessments).reduce((acc, id) => {
+      return {
+        ...acc,
+        [id]: {
+          ...oldState.assessments[id],
+          ...newState.assessments[id],
+        },
+      };
+    }, {} as AssessmentState),
+  };
+}
diff --git a/src/main/components/store/model-store.tsx b/src/main/components/store/model-store.tsx
index f5787e76..b463a602 100644
--- a/src/main/components/store/model-store.tsx
+++ b/src/main/components/store/model-store.tsx
@@ -30,6 +30,7 @@ import {
   Patcher,
 } from '../../services/patcher';
 import { UMLModel } from '../../typings';
+import { merge } from './merge';
 
 type OwnProps = PropsWithChildren<{
   initialState?: PreloadedState<PartialModelState>;
@@ -48,6 +49,7 @@ export const createReduxStore = (
     patcher &&
     createPatcherReducer<UMLModel, ModelState>(patcher, {
       transform: (model) => ModelState.fromModel(model, false) as ModelState,
+      merge,
     });
 
   const reducer: Reducer<ModelState, Actions> = (state, action) => {
diff --git a/src/main/services/patcher/patcher-reducer.ts b/src/main/services/patcher/patcher-reducer.ts
index 6cc32fc1..cbede062 100644
--- a/src/main/services/patcher/patcher-reducer.ts
+++ b/src/main/services/patcher/patcher-reducer.ts
@@ -1,6 +1,7 @@
 import { Reducer } from 'redux';
 import { Patcher } from './patcher';
 import { PatcherActionTypes } from './patcher-types';
+import { deepClone } from 'fast-json-patch';
 
 export type PatcherReducerOptions<T, U = T> = {
   /**
@@ -10,10 +11,21 @@ export type PatcherReducerOptions<T, U = T> = {
    * @returns The state in the internal schema.
    */
   transform?: (state: T) => U;
+
+  /**
+   * Merges the old state with the new state. This is useful when naive strategies
+   * like `Object.assign` would trigger unwanted side-effects and more context-aware merging
+   * of state is required.
+   * @param oldState
+   * @param newState
+   * @returns The merged state.
+   */
+  merge?: (oldState: U, newState: U) => U;
 };
 
 const _DefaultOptions = {
   transform: (state: any) => state,
+  merge: (oldState: any, newState: any) => ({ ...oldState, ...newState }),
 };
 
 /**
@@ -27,16 +39,14 @@ export function createPatcherReducer<T, U = T>(
   options: PatcherReducerOptions<T, U> = _DefaultOptions,
 ): Reducer<U> {
   const transform = options.transform || _DefaultOptions.transform;
+  const merge = options.merge || _DefaultOptions.merge;
 
   return (state = {} as U, action) => {
     const { type, payload } = action;
     if (type === PatcherActionTypes.PATCH) {
       const res = transform(patcher.patch(payload));
 
-      return {
-        ...state,
-        ...res,
-      };
+      return merge(state, res);
     }
 
     return state;
diff --git a/src/tests/unit/components/store/merge-test.ts b/src/tests/unit/components/store/merge-test.ts
new file mode 100644
index 00000000..a6211b0e
--- /dev/null
+++ b/src/tests/unit/components/store/merge-test.ts
@@ -0,0 +1,22 @@
+import { merge } from '../../../../main/components/store/merge';
+import { ModelState } from '../../../../main/components/store/model-state';
+import diagram from '../../test-resources/class-diagram.json';
+import diagram3 from '../../test-resources/class-diagram-3.json';
+
+describe('merge', () => {
+  const pkgId = 'c10b995a-036c-4e9e-aa67-0570ada5cb6a';
+  const class1Id = '04d3509e-0dce-458b-bf62-f3555497a5a4';
+  const class2Id = '9eadc4f6-caa0-4835-a24c-71c0c1ccbc39';
+
+  test('merges two model states.', () => {
+    const oldState = ModelState.fromModel(diagram as any) as ModelState;
+    const newState = ModelState.fromModel(diagram3 as any) as ModelState;
+
+    const merged = merge(oldState, newState);
+
+    expect(merged.elements[pkgId]).not.toBeDefined();
+    expect(merged.elements[class1Id]).toBeDefined();
+    expect(merged.elements[class2Id]).toBeDefined();
+    expect(merged.elements[class1Id].owner).toBeNull();
+  });
+});
diff --git a/src/tests/unit/components/store/model-state.test.ts b/src/tests/unit/components/store/model-state-test.ts
similarity index 100%
rename from src/tests/unit/components/store/model-state.test.ts
rename to src/tests/unit/components/store/model-state-test.ts
diff --git a/src/tests/unit/services/patcher/patcher-reducer-test.ts b/src/tests/unit/services/patcher/patcher-reducer-test.ts
index dfc9311d..f941f0e6 100644
--- a/src/tests/unit/services/patcher/patcher-reducer-test.ts
+++ b/src/tests/unit/services/patcher/patcher-reducer-test.ts
@@ -26,6 +26,18 @@ describe('test patcher reducer.', () => {
     expect(nextState).toEqual({ y: 42 });
   });
 
+  test('calls given merge function for applying the patch.', () => {
+    const cb = jest.fn((x, y) => ({ ...x, ...y }));
+
+    const patcher = new Patcher();
+    patcher.initialize({});
+
+    const reducer = createPatcherReducer(patcher, { merge: cb });
+    const nextState = reducer({ y: 41 }, PatcherRepository.patch([{ op: 'add', path: '/x', value: 42 }]));
+
+    expect(nextState).toEqual({ x: 42, y: 41 });
+  });
+
   test('handles weird options.', () => {
     expect(() => createPatcherReducer(new Patcher(), {})).not.toThrow();
   });
diff --git a/src/tests/unit/test-resources/class-diagram-3.json b/src/tests/unit/test-resources/class-diagram-3.json
new file mode 100644
index 00000000..8c1950a1
--- /dev/null
+++ b/src/tests/unit/test-resources/class-diagram-3.json
@@ -0,0 +1,90 @@
+{
+  "version": "3.0.0",
+  "type": "ClassDiagram",
+  "size": { "width": 860, "height": 260 },
+  "interactive": { "elements": {}, "relationships": {} },
+  "elements": {
+    "04d3509e-0dce-458b-bf62-f3555497a5a4": {
+      "id": "04d3509e-0dce-458b-bf62-f3555497a5a4",
+      "name": "Class",
+      "type": "Class",
+      "owner": null,
+      "bounds": { "x": 200, "y": 70, "width": 200, "height": 140 },
+      "attributes": ["90f94404-1fc6-4121-97ed-6b2c6d57d525"],
+      "methods": ["12d8bb82-e4e5-4505-a0eb-48ddab0fc0a0"]
+    },
+    "90f94404-1fc6-4121-97ed-6b2c6d57d525": {
+      "id": "90f94404-1fc6-4121-97ed-6b2c6d57d525",
+      "name": "+ attr: Type",
+      "type": "ClassAttribute",
+      "owner": "04d3509e-0dce-458b-bf62-f3555497a5a4",
+      "bounds": { "x": 80, "y": 110, "width": 200, "height": 30 }
+    },
+    "12d8bb82-e4e5-4505-a0eb-48ddab0fc0a0": {
+      "id": "12d8bb82-e4e5-4505-a0eb-48ddab0fc0a0",
+      "name": "+ method()",
+      "type": "ClassMethod",
+      "owner": "04d3509e-0dce-458b-bf62-f3555497a5a4",
+      "bounds": { "x": 80, "y": 140, "width": 200, "height": 30 }
+    },
+    "9eadc4f6-caa0-4835-a24c-71c0c1ccbc39": {
+      "id": "9eadc4f6-caa0-4835-a24c-71c0c1ccbc39",
+      "name": "Class",
+      "type": "Class",
+      "owner": null,
+      "bounds": { "x": 620, "y": 90, "width": 200, "height": 100 },
+      "attributes": ["dbd4193a-4483-43df-8934-77192be006c2"],
+      "methods": ["e7ef41ee-290e-4df2-a535-199f1c5521fd"]
+    },
+    "dbd4193a-4483-43df-8934-77192be006c2": {
+      "id": "dbd4193a-4483-43df-8934-77192be006c2",
+      "name": "+ attribute: Type",
+      "type": "ClassAttribute",
+      "owner": "9eadc4f6-caa0-4835-a24c-71c0c1ccbc39",
+      "bounds": { "x": 620, "y": 130, "width": 200, "height": 30 }
+    },
+    "e7ef41ee-290e-4df2-a535-199f1c5521fd": {
+      "id": "e7ef41ee-290e-4df2-a535-199f1c5521fd",
+      "name": "+ method()",
+      "type": "ClassMethod",
+      "owner": "9eadc4f6-caa0-4835-a24c-71c0c1ccbc39",
+      "bounds": { "x": 620, "y": 160, "width": 200, "height": 30 }
+    }
+  },
+  "relationships": {
+    "f5c4e20d-8347-4136-bc02-b7a016e017f5": {
+      "id": "f5c4e20d-8347-4136-bc02-b7a016e017f5",
+      "name": "",
+      "type": "ClassBidirectional",
+      "owner": null,
+      "bounds": { "x": 280, "y": 130, "width": 340, "height": 1 },
+      "path": [
+        { "x": 340, "y": 0 },
+        { "x": 0, "y": 0 }
+      ],
+      "source": {
+        "direction": "Left",
+        "element": "9eadc4f6-caa0-4835-a24c-71c0c1ccbc39",
+        "multiplicity": "",
+        "role": ""
+      },
+      "target": {
+        "direction": "Right",
+        "element": "04d3509e-0dce-458b-bf62-f3555497a5a4",
+        "multiplicity": "",
+        "role": ""
+      },
+      "isManuallyLayouted": false
+    }
+  },
+  "assessments": {
+    "04d3509e-0dce-458b-bf62-f3555497a5a4": {
+      "modelElementId": "04d3509e-0dce-458b-bf62-f3555497a5a4",
+      "elementType": "Class",
+      "score": 10,
+      "feedback": "good",
+      "label": "Class",
+      "labelColor": "blue"
+    }
+  }
+}