Steps to reproduce:

Create a new project from the Universal 3D (URP blank) template
Select GameObject > UI Toolkit > Standard Elements > Button
If the "Open visual element editing stage" dialog appears, click Continue
In the "Create UI Document" dialog, keep the default name "New UXML" and click Save
Select File > Save
In the Hierarchy, expand New UXML and select the Button
Select GameObject > UI Toolkit > Standard Elements > Label
Right-click the Label in the Hierarchy and select Open in UI Builder
In UI Builder, select File > Save, then close the UI Builder window
In the Hierarchy, select the Button, then select GameObject > UI Toolkit > Standard Elements > Toggle
Right-click the Toggle in the Hierarchy and select Open in UI Builder
In UI Builder, select File > Save, then close the UI Builder window
Quit the Editor. If the "Scene(s) Have Been Modified" dialog appears, click Save
Reopen the project and expand New UXML in the Hierarchy

Actual results: UI Builder shows the Toggle, but File > Save does not write it to New UXML.uxml and the "*" is cleared, so the Toggle is lost after reopening

Expected results: File > Save in UI Builder writes the Toggle to New UXML.uxml

Reproducible with versions: 6000.7.0a5, 6000.7.0b5, 7000.0.0a8

Can't test with versions: 6000.0.84f1, 6000.3.24f1, 6000.6.6f1, 6000.7.0a3 (in-scene UI authoring is not available), 6000.7.0a4 (blocked by ~~UUM-147501~~: UI Builder opens without the Toggle)

Tested on (OS): macOS 26.6.2

Notes:

The first UI Builder save (step 9) writes the Label; only the second session loses the edit
Saving with File > Save in the main Editor window instead of UI Builder writes the Toggle