I've run into this problem a lot. Here's the setup:

I'll pull selects in Final Cut Pro, reveal the clip in the Finder and import it into After Effects to work with. When I go back to Final Cut Pro, the clip will be offline for a brief moment before showing up again. What's worse is if I've rendered that clip somewhere in a timeline, that render will be gone.

I finally decided to dig into this to find out what was going on. It turns out it's a simple thing, really. When you load a clip into After Effects CS4, it appends XMP metadata to the file. Final Cut Pro then sees the updated file and takes a moment to relink what it thinks is new media. So there you go.

Moral of the story: be careful when working directly with FCP media files in After Effects.