I recently ran the 'Reorganize files in the folder "iTunes Music"' broke iMovie's link from my VFT movie to its music file! I had to manually copy the music back to and create its original folder. (Thankfully there was an error message telling me this, and telling me what the old folder (path) was!)
This caused strange problems in iMovie. The affected movies could only be played with music if a copy of it was in the Media Browser. But I could not export them anymore, as I would get the error message I referred to above. Not only that, but the playback in iMovie was of reduced quality. It was as if I had exported it to H.264 with the medium or medium-low quality setting! Oh, maybe because it had to get the sound from the copy in the Media Browser it had to use the video from that, too? Interesting. Can anyone verify this?
And I also got some un-removable keyword lines! Very strange. How could a missing music file cause so much damage?! OK, perhaps another blasted side effect of using 18 fps footage. Even so.
So be warned: If you run the 'Reorganize files in the folder "iTunes Music"' function, you might break some of your movies. Evidently the reference is by name, not inode number.