The broken Prefab Variant Variant GameObject remains when its parent Variant is recreated

Steps to reproduce:

1. Create and open a new project
2. In Preferences, enable the new Hierarchy
3. Create and make a prefab of a Cube GameObject
4. Create a Cube Prefab Variant and another variant of the Cube Prefab Variant
5. Instantiate the last Prefab Variant
6. Delete the first Cube Variant in the Project
7. Create a Prefab Variant of the Cube again
8. Observe the Hierarchy

Actual results: The broken version of the Variant stays in the Scene

Expected results: The broken version of the Variant is replaced by the new version of the Variant

Reproducible with versions: 6000.3.0a6, 6000.3.17f1, 6000.4.11f1, 6000.5.0a6

Not reproducible with versions: 6000.5.0b12, 6000.6.0a7

Can’t test with versions: 6000.0.77f1 (No new Hierarchy)

Fixed in: 6000.5.0a7

Tested on (OS): Windows 11 Pro (25H2)

Workaround: Close and open the Hierarchy window

Notes:

• Not reproducible in the old Hierarchy
• Trying to do any action on the broken GameObject (right-clicking, deleting, ranaming) results in NullReferenceExceptions