One of the changes we made in the PR you referenced, is to correctly calculate environment ambient lighting. We were previously using a blurry glossiness as ambient. The new calculation usually doesn’t change ambient significantly, but perhaps in your case it does.
It is possible to generate ambient using the old method (see here).
I created a quick example which generates legacy ambient on the scene, then flips between old and new lighting. Check it out here.
Feel free to fork that project and try it with your own cubemap.
So I tried out the method of regenerating the prefiltered atlas, and eventually even copying your script because I could not see a difference. When I copied you script, I could see the change, but it was pretty subtle. Were there other changes that could be affecting the skybox light that I might be able to play with? The materials still appear correctly in 1.50.2
Unfortunately it’s almost impossible to say without being able to inspect the scene and compare differences. If you’re able to create a slimed-down scene that we can investigate further that would really help.