well, I won't do this again, but I'm trying to figure out the what/why/how...
I had an animation completed, using a layered Illustrator file imported as a composition (retain layer size setting). I then realized I had missed a bit of info in my original illustrator file, so I resized my AI art board (mistake) to fit in this new info, then I added that new AI layer into my AE comp.
Then, things went terribly wrong--AE layers are now being partially masked, in unlogical ways, and I have no clue how to fix it. Probably starting over.
Anyhow, can someone shed some light on this? Is this just a rule I shouldn't have broken?
Changing the artboard size changes the artboard origin (which as of CS6 is separate from the global origin and per artboard) and thus the relative placement. This would change the coordinates of course that AE sees. Compensating the origins may recover your file therefore.