Prefabs collapsing into normal GameObjects when restarting Editor

[Tweety-Lab]

Describe the bug
When restarting the Editor, opening a scene that contained Prefabs results in all Prefabs being collapsed into regular GameObjects. Their links to the original Prefabs are lost, and they no longer retain their prefab connection.

To Reproduce
Steps to reproduce the behavior:

1. Create a new project
2. Add a Prefab to the scene and save it
3. Restart Editor
4. Reopen the saved scene

Expected behavior
Prefabs retain their Prefab Link and continue to be prefabs across restarts.