After upgrade, iTunes complaints with "original file could not be found"

Question

After upgrading to 8.2.0.23, a large number of songs now have a ! in them and if I try to play them, iTunes will say with "The song xxx could not be used because the original file could not be found." This has happened to me before but never to this large number of files.
If it were only a handful of songs it wouldn't be an issue because iTunes allows me to locate it manually, which for first time, iTunes opens the dialog in the directory where the file is. I can click on the mp3 file and that's it. Problem is that from the on, the dialog opens in the same directory as the first song, which makes it very hard to navigate to the directory where the second song is (unless it's the same album of course). Multiply that by 1000 and it's an impossible task.
I've found that the problem is neither the itl file nor the xml file. I already tried the previous itl file and the problem persists.
After comparing the files that are OK with those missing in the .xml file, I found that iTunes is somehow messing up the location tag for files with underscores in the filename. For example, 01_mysong.mp3 gets replaced to 01%20-%20mysong.mp3 in the location tag in the xml file. If use iTunes to locate the file, which as I mentioned above fixes the issue, the location tag gets updated to the correct filename and a bunch of hex numbers get added to the comments tag.
Now, if I exit iTunes and change the location tag to the correct filename in the xml file with a text editor, iTunes magically messes up the tag again when it comes up.
I tried unchecking the "Keep iTunes Music folder organized" but that didn't help.
At first I thought it was an issue with the comments tag and that only mp3 files downloaded from Amazon had the problems. It seems that ALL those songs have the problem but there are a few other songs I got from the iTunes store that are also messed up.
I have not moved any songs at all, this just happened all by itself after upgrading.
I also tried re-adding the folders where all the Amazon mp3 files are, but this created duplicate entries in the library. Unfortunately, even though the new entries do play, they don't have ratings or play count.
Is there any way I could fix this without losing my ratings and play counts and without having to manually fix every song one by one?
I'll appreciate any hint you can provide.
Thanks

Answer 1

I have the same problem except almost every song I bought from Itunes has this problem. Not only that, but somehow some of the music, about $125 worth has been deleted form my 3 back up discs. This is only happening with my purchases and not any songs I uploaded from cd. How on earth did this happen, and how did it wipe clean 3 different back ups? I have found some of the music where it belongs, but like I said some of them are gone, gone, gone. I run three different back ups and they are on 24/7. Where is all of this music? I still have it on my ipod, but it will not load back into itunes the way purchases used to. Some of the music is purchased straight to my ipod touch, but shouldn't i be able to reload them into itunes? I spent 3 hours going 1 song at a time reloading them from their original location. But I cannot locate about $125 worth of music that I purchased from itunes. I have 6 macs in my family and preach the good news to all who will listen about hows macs are flawless. Now I have egg all over my face and have thrown away a nice sum of money on missing music. Please help!