Here's a shot in the dark:
Is this Illustrator file on another disk drive?
I ask this only because the one other time when I recall seeing this error, it was resolved by moving the Illustrator file to the local disk that the project file was on.
All the project files are on an internal RAID volume inside the MacPro.
The RAID volume isn't having any problems and the other project files seem fine.
Including rendered out quicktime clips. They play fine.
This is an issue with AI and ultimately therefore also the AI routines that AE shares to access such files. Has been there forever and neither the AI people nor the AE team seem to be able to fix it in a consistent manner. Simply save a copy of the file from AI, then use Replace Footage instead of reload or at least always fully reload the AE project.
This happens to me sometimes when I import files from a mac through my windows pc. The names of the folder have occult strange characters. If you erase the names of the folders and/or the files an you type it again, then the problem dissapear.
Hope this help!
I've just had this problem too and it happened when I moved the project files from one place on my hard drive to another.
I solved it by just performing 'Replace footage' and choosing the offending file again, this sorted the problem.
Fixed the problem, it's a simple folder structure issue. When you have your assets placed in too long of a file path After Effects freaks out and can't find them. Just place the folder on your main drive, on the desktop. Make it so the computer takes the least amount of steps to locate everything.