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ie. do I have to set the materials nested inside the precomp, or can I just change them in the precomp settings, and if so is there a magic button I'm supposed to click to get the precomp to obey settings like accept shadows, etc?
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Nope. AE works upstream in 3D, not downstream. Settings from sub-comps are propagated to the parent comp, not the other way around. You have to tweak your materials in the pre-comps, even if in a funny way of inconsistent logic it will still use the lights from the parent comp and messing with layer switches can still make all sorts of a mess...
Mylenium
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Thanks Mylenium, I thought that was the behavior I was getting, but I couldn't quite tell from just moving a light around. I'll remember to set the materials how I want them first and duplicate from now on, instead of setting them later, or create a global control parent for contents inside the precomp.