Today I had the same problem and found this thread.
Obviously you have solved or you no longer need advise, but i found something that doesn’t solve your problem but is a tip not to fall in. I hope not saying something banal.
The problem when using media that FCP X link to, with other apps is the fact, like someone said, of the “Last Modified” problem, so the metadata related to.
I’ve had your same problem using a Quicktime file in After Effects, saving the project in AE, and so lost the link immediately in FCP X. So i tried with another QT, but before do this I set the “Sharing & Permission” of this file to “Read only”, and this solve my problem, I can use it in AE or whatever apps and FCP X mantain all links.
I think this can only solve QT problems, or movie in general, because I usually don’t need to write to a movie file itself. In my opinion it doesn’t works with other assets like graphics or audio (psd, png, audio) where maybe you have to update regularly the file.