Reproduction steps:
1. Open the attached project "ReproProj"
2. In the Project window, select the “UXMLTest3”
3. In the Inspector, there shouldn't be any Warnings present
4. Move “UXMLTest2” into a different folder i.e. “UI Toolkit” folder
5. Select “UXMLTest3” again and there should be a warning that has an option to "Apply (Overwrite File)"
6. Double click UXMLTest3 and in UI Builder, right click the Visual Element in the Hierarchy window and create a template
7. Save and close down the UI Builder
8. Move the created template into a different folder and select “UXMLTest3”
9. Observe the Inspector

Expected result: The option to "Apply (Overwrite Files)" is available
Actual result: Warning and "Apply (Overwrite File)" Button is not present

Reproducible with: 6000.0.55f1, 6000.2.2f1, 6000.3.0a6

Testing environment: Windows 10 Enterprise 21H2, Windows 11 (user reported)
Not reproducible on: No other environment tested