I can't find any reference to this particular case type, among the zillion ways iTune messes it all up. I read of files being moved to some other dir, re-encoded, re-sized (imgs), removed from collection but not from disk, removed form iPod/Phone after sync, removed from both HDD and mobole device after sync, or to collections partially deleted due to some user's mistake / GUI poor design.

The weird thing is that my friend is positive he has not been synching his iPod from work PCs since before this supposedly happened. So, while I tend more and more to believe that iTune is responsible, it really seems something unusual happened even for iTunes.

Also, to add more info, in both the empty directories my friend found not a "file" as he originally mentioned, but a directory tree replicating the iTune collection structure, it seems.

This is horrble software design, beyond compare.