I'm sure we all run into this where we need to add or delete layer(s) in a source Illustrator file. It always throws AE off thinking its missing frames or dimensions of a layer are wrong.
With CS5, I think AE handles this a little more gracefully with PSD files. But any tips on making nice with modified Illustrator files?
(I usually just end up re-importing the entire file as a new comp)
Create a ton of empty layers with just a rectangle or circle on them and use them as a placeholder. the fault is with AI's poorly structured file format, not so much AE and that is the safest way to avoid any issues.