fix(mongo): ensure JSON values are properly diffed

Closes #5572

packages/mongodb/src/MongoPlatform.ts

@@ -65,7 +65,7 @@ export class MongoPlatform extends Platform {
   }
 
   override convertJsonToDatabaseValue(value: unknown): unknown {
-    return value;
+    return Utils.copy(value);
   }
 
   override convertJsonToJSValue(value: unknown): unknown {

tests/features/custom-types/GH5572.test.ts

@@ -0,0 +1,40 @@
+import { Entity, MikroORM, PrimaryKey, Property } from '@mikro-orm/mongodb';
+
+@Entity()
+class Dummy {
+
+  @PrimaryKey()
+  _id!: number;
+
+  @Property({ type: 'json' })
+  a!: { b: number };
+
+}
+
+let orm: MikroORM;
+
+beforeAll(async () => {
+  orm = await MikroORM.init({
+    dbName: '5572',
+    entities: [Dummy],
+  });
+  await orm.schema.refreshDatabase();
+});
+
+afterAll(async () => {
+  await orm.close(true);
+});
+
+test('deep update', async () => {
+  const usr1 = orm.em.create(Dummy, { _id: 1, a: { b: 1 } });
+  await orm.em.flush();
+  orm.em.clear();
+
+  const usr2 = await orm.em.findOneOrFail(Dummy, usr1._id);
+  usr2.a.b = 100;
+  await orm.em.flush();
+  orm.em.clear();
+
+  const usr3 = await orm.em.findOneOrFail(Dummy, usr1._id);
+  expect(usr3.a.b).toBe(100);
+});