Music files missing? Seems like iTunes bug...

Question

I recently noticed that many of my music files are missing, and that the selection appears to be somewhat random. They are retained in iTunes, but have the ! next to them. So, doing the logical thing, I tried to locate them, and the files themselves are missing, but their iTunes link is preserved.
In an effort to continue to do the logical thing, I then systematically went through my CD library, re-loading all the missing material back into iTunes. This was extremely tedious, but appeared to fix most of the issues (obviously, the ones were the CD case was mysteriously empty were left unfixed). The files played fine at that time. Then I carried the computer upstairs to my home office, where I proceeded to plug it in to do a time machine backup on the newly transferred files.
Now here's where it gets really strange... The time machine backup went swimmingly without hitches, to a relatively new USB 3.0 drive. I then set about organizing the music, so that it would all be in the iTunes music folder (User(me)/Music/iTunes/iTunes Music/ directory, the one automatically made by iTunes on installation). Many of the songs linked perfectly, and I didn't have to re-link the songs to their new location, as one might expect. So, I then thought I would sit down to enjoy this new library that I had spent a day bringing up to speed and organizing again. And, low and behold, songs are missing--again. Not just the ones that I couldn't replace, but some of the newly replaced ones. For example, Track 12 of an album might be missing, but the files for Tracks 1-11 and 13+ are all present.
As other people who have experienced this problem previously have noted, there does seem to be a slight preference for songs whose artist and/or title include accented characters, although my detection ability is more limited now, as I have since lost many of these original CDs, and so the songs were not replaced within the library. But, while they account for about 5-10% of my overall library, they accounted for about 50% of the songs missing at the beginning of yesterday's overhaul.
And what makes matters really strange is that when I tried to look up the missing files--which I know myself to have imported yesterday--in the fresh time machine backup I made right after importing all that music, they are all missing.
So, it appears that iTunes is systematically deleting files at random. While I'm tempted to try to put the missing ones back on (fewer are "re-missing" than I was able to replace, so it's a little better), this doesn't exactly seem fruitful, given the fresh deletions.
The original music files were encoded a long time ago, and have been copied and re-copied (and recopied... ad infinitium). It appears that everything that I encoded on the really old system (before iTunes really became popular for this sort of thing) were preserved; however, the issue seems to temporally localize around the time I started using iTunes for most of my music encoding needs (except, of course, for the little issue about files that were imported less than 24 hours ago).
A few other notes:
- I did not delete these files accidentally. I'm more careful than that.
- The files are not there (they're not just hidden--I already checked for this).
- iTunes has retained the link to where it believes the file should be.
- The issue appears to have originally arisen quite some time ago, as these files are systemically missing from all backups made by time machine. However, it wasn't all that long ago that I deleted my entire library and started over (about 2 years, so the files should have been natively present on 2 of my macs) by re-importing all the files in my music folder. This newly created library has since become the "master" library that is propigated to all my other computers (although I don't trust iCloud for obvious reasons, given this fiasco--Thanks, Apple...)
- I have not elected to have iTunes manage my music folder, or automatically copy things to the iTunes music folder when importing (although this is the default destination, so they are imported there, but not duplicated there when imported from elsewhere on the hard drive).
- I am currently running OS X 10.6.8 on an Intel Mac (yeah, yeah, I'd upgrade the OS, but software that cost more than the computer isn't 10.8--or even 10.7--compatible).
If anyone has any thoughts on how to prevent this issue in the future, I'd really appreciate it. I think the music files themselves are just... gone. But, I would like to be able to have them stick around for a bit when I get around to dedicating another day to trying to import them from their CD.
Does anyone know a piece of third party software that allows you to sync and update iDevices? Hopefully one that doesn't take over my music library and decide to delete things of its own accord?

Answer 1

I was lucky to be able to use a PC, that after trying numerous times actually read the external hdd, I quickly copied all files over to a backup hdd and recovered all files. After that I ended up in contact with Western Digital about the incident and they recommended to completely erase (7-pass erase) of the hdd, which ended up taking over 5 days to do. They gave me no reason as to "Why" it would have happened but if I erase and reformatted of the hdd and the problem reoccurred they recommended to get the unit replaced.
I was lucky to recover all my files.....keep trying on different computers if you can, and copy what you can get hold of. The 7-pass erase will delete pretty much every trace of information on the hdd with no chance of recovery.
So far since the incident its been running ok but I not longer trust the hdd to be stable. Not a simple nor quick process / solution I'm afraid.
Good luck!
Once you have recovered your files (or as many as you can get hold of) and ready to erase the hdd:
(THIS WILL ERASE ALL YOUR DATA, MAKE SURE YOU HAVE A BACKUP BEFORE PROCEEDING)
Connect the drive directly to the Mac, open Disk Utility.
Select the drive and click on the "Erase" tab Select the "7-times zeros" to completely erase the drive.
Once the erase have completed format the drive to your selection.