Reproduction steps:
1. Open the attached “BugRepro” project
2. Open the “Assets/Empty.unity” Scene
3. Open the “Assets/ModifyAuto.unity” Scene
4. Observe the Console window
5. Re-open the “Assets/ModifyAuto.unity” Scene
6. Observe the Console window

Expected result: Nothing gets printed
Actual result: “Applying modified properties!” message is printed

Reproducible with: 2021.3.43f1, 2022.3.45f1, 6000.0.18f1

Reproducible on: Windows 11
Not reproducible on: No other environment tested

Notes:

* If the scene is open and you force the editor to recompile, the changes are recognized and saved as expected
* When the same code is executed via the context menu, the data is correctly saved