When using CS5 I was able to insert new layers in my Illustrator document without causing a problem with After Effects. I could just load the new layer, re-load any other layers where I had made changes and all was well.
Now I have CS5.5 and inserting a layer into Illustrator anywhere except at the top will cause After Effects to display the contents of another layer, cropped to the size of the correct layer. Reloading does nothing. I have to go, and one by one, painstakingly replace footage with each layer above where I had made the change in Illustrator. Same layer name and all, but replacing footage works, reloading doesn't.
I have an AI file with about 100 layers on one artboard, after having issues with separate artboards in AE.