Elements remain in the UI Toolkit's editing stage and cannot be edited when the elements are opened in UI Builder, deleted and saved

Steps to reproduce:

1. Create a new Unity project using the Universal 3D template
2. Create a new Button in the Hierarchy window (Right-click > UI Toolkit > Standard Elements > Button)
3. Enter editing stage by clicking the "Continue" butotn
4. Save
5. Right-click the Button and select "Open in UI Builder"
6. Delete the Button in UI Builder
7. Save and exit the UI Builder
8. Observe the Hierarchy window
9. Try editing the Button's settings in the Inspector
10. Observe the Inspector

Actual results: The Button remains in the Hierarchy even after being deleted and saved in UI Builder, changing the Button's settings in the Inspector is not responsive, sometimes it changes, sometimes it does not, and sometimes a "IndexOutOfRangeException" error is thrown

Expected results: The Button is deleted

Reproducible with versions: 6000.6.0b5, 6000.7.0a3

Can’t test with versions: 6000.0.80f1, 6000.3.20f1, 6000.5.5f1 (due to feature missing)

Tested on (OS): MacOS Silicon Tahoe 26.5.1