friendly, the same kind of thing happened to me a while ago. I have 20000+ files, and one day i noticed an album was missing a few tracks. Then to my shock, I realised I was missing a thousand or so files. Like you're saying, it seemed totally random. The only thing I realised was that all the files that were deleted were imported during a similar period. They'd all been imported within the past few months. I have playlists saved for every imported month, and many backed-up libraries, so it wasn't too hard to regain the missing tracks. I alter file properties in MC9 but don't alter the id3 tags themselves so having the backed-up libraries was a HUGE relief.
The same thing happened one or two more times though, with the same files were missing I'm quite sure.
Since then, I've formatted my system drive, installed a new version of MC9 and had no problems.
At the time I think I was using MC9.0.172. I also had a network with MC9 installed on both systems. For some reason I felt that files went 'missing' after someone tried to play tracks on MC9 on the other system (with all mp3s being stored on this one). Perhaps not, but I was quite sure the problem had to do with the network, I'd only just set it up when the files starting to go 'missing'.
Anyway, hopefully what I've said has helped you in some way. Feel free to ask me any questions, and good luck re: the re-importation.