E3D does not support collapse transformations. You are most definitely making a mess somewhere. On the other hand this could of course be a graphics hardware issue, but your info is not sufficient. You need to provide screenshots and proper system info.
I may be misunderstanding your setup, but you can't precompose cameras to share Z depth between comps.
If you want Particular and Optical Flares to react appropriately, you will either need to place those layers in the same comp as your Element layer, or use expressions to link cameras between both comps.
If I've misunderstood, please post a more detailed description and/or screen grab of your timelines.
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Thanks for your answers! I think you both misunderstood me.
Anyway, it was my fault, the Element 3D layer on the main comp had turned into a guide layer for some reason, and that's why its duplicate on the precomp (also a guide layer) didn't appear on the main comp.