I think I may have changed the positioning slightly in the parent comp. ignore BG colours I added the background (created in Particular) into the parent comp. The BG in the precomp is just a colour I selected when i created the composition originally.
The colour change on the actual logo is a mystery thought. I assumed it was because all the lighting etc is set up in the pre comp?
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.