Reproduction steps:
1. Create a new project and make sure new Hierarchy window is enabled
2. Enable Hierarchy Integration in Project Settings (Edit > Project Settings… > UI Toolkit)
3. GameObject > UI Toolkit > UI Document
4. Enter and exit Play mode
5. Observe UIDocument GameObject in the Hierarchy

Actual result: All GameObjects under UIDocument disappear
Expected result: All GameObjects under UIDocument remain visible

Reproducible with: 6000.5.0a5, 6000.5.0a6
Not reproducible with: 6000.3.7f1, 6000.4.0b7, 6000.5.0a4
Couldn’t reproduce with: 6000.0.66f2 (No Enable Hierarchy Integration option)

Reproduced on: macOS Sequoia 26.2 (M4)

Note: Disabling and reenabling Enable Hierarchy Integration option makes GameObjects reappear