Reproduction steps:
1. Open the attached “BugRepro” project
2. Open the “Assets/Scenes/SampleScene” Scene
3. In the Hierarchy window, select “Cube” GameObject
4. In the Inspector window, change Position X property to 10
5. Enter Play Mode
6. Open the “Assets/Scenes/TestScene” Scene

Expected result: A “Scene(s) Have Been Modified” pop-up window appears, asking if you want the changes to be saved
Actual result: No pop-up window appears and all changes revert

Reproducible with: 2022.2.0a13, 2022.3.24f1, 2023.2.18f1, 6000.0.0b14
Not reproducible with: 2021.3.37f1, 2022.2.0a12

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

Note: In step 4, any changes to the Scene will do, this is only an example