Thank you for coming back to post your postmortem update!
This also gets into what is the current active scene, which is the one used for lighting, which of course in turn also controls fog.
Here’s more related ramblings about multiple scene setups:
Additive scene loading is one possible solution:
https://discussions.unity.com/t/820920/2
https://discussions.unity.com/t/820920/4
https://discussions.unity.com/t/824447/2
A multi-scene loader thingy:
My typical Scene Loader:
Other notes on additive scene loading:
https://discussions.unity.com/t/805654/2
Timing of scene loading:
https://discussions.unity.com/t/813922/2
Also, if something exists only in one scene, DO NOT MAKE A PREFAB out of it. It’s a waste of time and needlessly splits your work between two files, the prefab and the scene, leading to many possible errors and edge cases.
Two similar examples of checking if everything is ready to go: