How to reproduce:

1. Create a new project
2. Enable “Use new Hierarchy window” in Edit -> Preferences -> General
3. Create two scenes
4. Add both of them to the Hierarchy
5. Unload one of them
6. Enter and Exit Play Mode
7. Observe the Hierarchy

Actual result: The unloaded scene is not present in the Hierarchy
Expected result: The unloaded scene is present in the Hierarchy

Reproducible in: 6000.3.0a6, 6000.3.5f1, 6000.4.0b5, 6000.5.0a5
Could not test in: 6000.0.66f1, 6000.3.0a1 (New Hierarchy window not introduced yet)

Reproduced on: Windows 11 Pro (25H2)
Not reproduced on: No other environment tested

Workaround: Close and re-open the Hierarchy window

Notes:
- Does not reproduce on the old Hierarchy window
- The unloaded scene disappears already when entering Play Mode, and doesn’t return after exiting it