Hi all. I've been going through this as well and have some thoughts about it.
I started noticing the exclamation points a while ago, but figured that iTunes had just lost track of things and I'd fix it later. (My iTunes music folder was in an unusual location.)
Last night I installed iTunes 11 and noticed the exclamation points again. This time I decided to fix them. A few of the files I found hiding in various places on my HD (but not in the iTunes Music folder... weird). So I told iTunes where they were and got them into the iTunes Music folder and that part is fine. But... a bunch of the files were just GONE. Nowhere on the drive at all. I did not delete them (intentionally -- but read on) and would not have -- a few are irreplaceable (songs recorded by friends, etc.)
The majority of the library (several thousand tracks) was intact, but these few hundred missing tracks worried me. How could they be gone? They are still on my iPod -- I've listened to some of them in the last week. The iPod (old 5G Video) last synced a couple of weeks ago. Which is after the exclamation points appeared.
For many of them, I tried to "get info." Then iTunes would tell me it couldn't find the track, and did I want to locate it? I clicked "no" and it then went into the info panel. And I noticed that iTunes thought they all had a weird location. It said they were in a folder on a networked drive (let's call it "netdrive 1", and the folder was called "itunes-test-delete"!
Now, that network drive has been gone for maybe 2.5 years now. But it was just called "netdrive", not "netdrive 1". I can't think of any reason why there would have been an itunes-test-delete folder in it, but sometimes my spouse would work on the Mac as well.
So the first weirdness -- the location is one that hasn't existed for a couple of years, and the drive name shouldn't have a 1 at the end. It must have mounted as a duplicate drive, somehow. But if the files have been gone for two+ years, why are they still on the iPod after multiple syncs over the last couple of years?
So then I noticed something else. Every single missing file ended in " 1.mp3". So, for example, it might be named "daves_song 1.mp3" or "dance_song 1.mp3." This means... that they were all duplicate files at some point. (It's possible to just rename them with a 1, of course, but with all of them named that way, it's more likely they were all dupes.) All of them were duplicates of existing files on my system when they were created.
And now I think I know what may have happened. This is just a theory, but:
1. One of us, maybe my spouse, duplicated some songs to experiment on the network drive a few years ago (the itunes-test-delete folder which was apparently on a drive that no longer exists).
2. The files were deleted when the test was done, but after they had been added to the iTunes library. iTunes didn't know they were gone. The network drive itself eventually went away, too.
3. At that point the library had a bunch of duplicate songs listed. One existing track and one phantom track for each of these songs.
4. At some point, the duplicates annoyed me. I had iTunes search for duplicates and deleted some.
5. So... my theory is that instead of deleting the phantom tracks, I deleted the real ones, leaving phantom tracks in their place in the iTunes Library. I had no reason to notice a problem immediately -- iTunes thought they were still there until it eventually tried to play them, and unless I was actually watching it at the time, I wouldn't notice they were missing.
6. And perhaps the reason they stayed on the iPod is because the originals were already there and the dupes had never gotten to the iPod in the first place (quite likely as I used to manually maintain my iPod before I started letting it just sync), and as far as the iTunes Library was concerned, those songs were still on my drive, so no need to delete them when syncing.
As I said, this is just a theory. But do any of you think something like this might have contributed to your problem? (And is it likely to have caused mine?) Any of you prune any duplicates before you noticed tracks with the exclamation point? Also, do your exclamation-point tracks show a URL that is on a network drive that is no longer connected?
The good news is that the tracks were on the iPod and I could use a third-party tool to get them back. The bad news... when I plugged in the iPod tonight I got the dreaded "iTunes cannot read the contents of the iPod"... That's what you call good timing. Even better, my Time Machine backup machine was hosed recently. It's back up again, but it doesn't have any old backups old enough to help, since it's only got the last few weeks. Sigh.
All the tracks are still on the iPod, just the iTunesDB on the iPod is hosed. So I'm working on solving that. But that's another topic entirely. I think the disappearing files are because iTunes doesn't know which files are legit.