The only related problem I've ever had is this:
I have MC set to rename and move files to an external drive.... Sometimes I've found that if I've used MC to perform this function but I've forgotten to turn my external drive on, the files that I'm trying to move will vanish (i.e., MC does not give a warning saying "the destination drive/folder does not exist or is not accessible; it just rips/renames/moves the file as it's supposed to, except that since the destination drive isn't on, there's nowhere for the file to go, so, seemingly, it's disappears instead, with MC noting that the operation failed... making the file seemingly vanish). At least, they have in the past -- I haven't tested this on any recent MC builds though, because, well, I just try to remember to keep my external drive on when I'm renaming tracks, and that solves the problem.
I wonder if "missing" tracks like this end up going into some temp folder when a rename-and-move operation doesn't work as expected?