diff --git a/packages/core/src/hydration/ObjectHydrator.ts b/packages/core/src/hydration/ObjectHydrator.ts
index d1149eb6db32..b10292092a56 100644
--- a/packages/core/src/hydration/ObjectHydrator.ts
+++ b/packages/core/src/hydration/ObjectHydrator.ts
@@ -24,9 +24,10 @@ export class ObjectHydrator extends Hydrator {
    */
   hydrate<T>(entity: T, meta: EntityMetadata<T>, data: EntityData<T>, factory: EntityFactory, type: 'full' | 'returning' | 'reference', newEntity = false, convertCustomTypes = false, schema?: string): void {
     const hydrate = this.getEntityHydrator(meta, type);
+    const running = this.running;
     this.running = true;
     Utils.callCompiledFunction(hydrate, entity, data, factory, newEntity, convertCustomTypes, schema);
-    this.running = false;
+    this.running = running;
   }
 
   /**
@@ -34,9 +35,10 @@ export class ObjectHydrator extends Hydrator {
    */
   hydrateReference<T>(entity: T, meta: EntityMetadata<T>, data: EntityData<T>, factory: EntityFactory, convertCustomTypes = false, schema?: string): void {
     const hydrate = this.getEntityHydrator(meta, 'reference');
+    const running = this.running;
     this.running = true;
     Utils.callCompiledFunction(hydrate, entity, data, factory, false, convertCustomTypes, schema);
-    this.running = false;
+    this.running = running;
   }
 
   /**
diff --git a/packages/core/src/unit-of-work/ChangeSetPersister.ts b/packages/core/src/unit-of-work/ChangeSetPersister.ts
index 81f5e1f8fe37..016eaa79df06 100644
--- a/packages/core/src/unit-of-work/ChangeSetPersister.ts
+++ b/packages/core/src/unit-of-work/ChangeSetPersister.ts
@@ -282,6 +282,9 @@ export class ChangeSetPersister {
       return;
     }
 
+    // skip entity references as they don't have version values loaded
+    changeSets = changeSets.filter(cs => helper(cs.entity).__initialized);
+
     const $or = changeSets.map(cs => {
       const cond = Utils.getPrimaryKeyCond<T>(cs.originalEntity as T, meta.primaryKeys.concat(...meta.concurrencyCheckKeys)) as FilterQuery<T>;
 
diff --git a/tests/issues/GH4122.test.ts b/tests/issues/GH4122.test.ts
index ef32b6cfa35c..c64192c7f6e8 100644
--- a/tests/issues/GH4122.test.ts
+++ b/tests/issues/GH4122.test.ts
@@ -5,8 +5,10 @@ import {
   Ref,
   OneToOne,
   OptionalProps,
+  SimpleLogger,
 } from '@mikro-orm/core';
 import { MikroORM } from '@mikro-orm/sqlite';
+import { mockLogger } from '../helpers';
 
 @Entity()
 export class Book {
@@ -22,6 +24,9 @@ export class Book {
   @OneToOne({ entity: () => Book, mappedBy: 'prequel', ref: true, nullable: true })
   sequel?: Ref<Book>;
 
+  @Property({ version: true })
+  version!: number;
+
   @Property()
   title!: string;
 
@@ -33,23 +38,46 @@ beforeAll(async () => {
   orm = await MikroORM.init({
     dbName: ':memory:',
     entities: [Book],
+    loggerFactory: options => new SimpleLogger(options),
   });
   await orm.schema.refreshDatabase();
 });
 
 afterAll(() => orm.close(true));
 
-test('4122', async () => {
-  const book1 = orm.em.create(Book, { id: 'book1', title: 'book1' });
-  const book2 = orm.em.create(Book, { id: 'book2', title: 'book2', prequel: 'book1' });
+beforeEach(async () => {
+  await orm.schema.clearDatabase();
+  orm.em.create(Book, { id: 'book1', title: 'book1' });
+  orm.em.create(Book, { id: 'book2', title: 'book2', prequel: 'book1' });
   await orm.em.flush();
   orm.em.clear();
+});
+
+test('updating versioned reference (4121)', async () => {
+  const refetchedBook1 = await orm.em.findOneOrFail(Book, { id: 'book1' });
+  refetchedBook1.title = 'updatedBook1';
+  refetchedBook1.sequel!.unwrap().title = 'updatedBook2';
+  await expect(orm.em.flush()).resolves.not.toThrow();
+});
+
+test('extra updates (4121)', async () => {
+  const refetchedBook1 = await orm.em.findOneOrFail(Book, { id: 'book1' });
+  refetchedBook1.title = 'updatedBook1';
+  const mock = mockLogger(orm);
+  await expect(orm.em.flush()).resolves.not.toThrow();
+  expect(mock.mock.calls).toEqual([
+    ['[query] begin'],
+    ["[query] update `book` set `title` = 'updatedBook1', `version` = `version` + 1 where `id` = 'book1' and `version` = 1"],
+    ["[query] select `b0`.`id`, `b0`.`version` from `book` as `b0` where `b0`.`id` in ('book1')"],
+    ['[query] commit'],
+  ]);
+});
 
+test('4122', async () => {
   const qb = orm.em.createQueryBuilder(Book);
   await qb.update({ title: 'updatedTitle' }).where({ sequel: null });
 
-  await orm.em.refresh(book1);
-  await orm.em.refresh(book2);
+  const [book1, book2] = await orm.em.find(Book, {});
   expect(book1.title).toEqual('book1');
   expect(book2.title).toEqual('updatedTitle');
 });