Steps to reproduce:

1. Open attached project
2. Drag both scenes to hierarchy to enable multi scene editing
3. Open Occlusion culling tab and bake occlusion culling
4. On keyboard, press ctrl+s to save changes made to the scenes
5. Notice multiple errors in the console:
Cross scene references are not supported: 'SceneSettings' in scene 01 has an invalid reference to 'Cube (4)' in scene 02. This reference will not be saved in the scene.

Not reproducible: 5.3.2f1
Reproduced with: 5.3.2p1, 5.3.4p3, 5.4.0b14