I’m curious about collapse transformations “making the sky fall in” and having everything “lose its 3d character” that you mentioned in your first post. That shouldn’t happen. If you have a comp in your parent comp, it should still work. In fact, layers in the precomp should be able to interact with layers in your parent comp.
Have you tried rerendering the precomp to see if that changes things? That would let you know if the issue has to do with the layer setup/3d-ness/etc. in your precomp or if something is happening in your main comp to cause it.
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