Using iPod as transferring device damaged song files

Question

I searched the forum for an hour-hour and a half, and haven't found anything.
Here's the basis of what happened: I dragged my user folder by accident, and I needed to reinstall OS X. I usually transfer files with my iPod, and it always works, except this time. This time, I had many files that I needed to save, so I put them on the iPod, but deleted the music off it. I didn't know I could get it off the iPod (With Mac, recent one month switcher), so I deleted the songs in iTunes, so I would have enough space. Once I reinstalled, I connected the iPod and got the music files. They were all damaged in some way, some completely unusable. Is there any reason why this would happen? It's Mac formatted, and it has been flawless for a year. I'm usually very tech-savvy, but didn't expect any of this. I backup my songs as data on iPod when I am going to transfer them. Is there anyway to "undamage" the files, or do something else? I'm basically just looking for how/why this happened.
I made a very long email to Apple, but I didn't receive a response. Here it is, more details.
"I moved my User folder by accident and my settings got messed up, so I had to reinstall Mac OS X 10.4. Before I did that, I copied all my files onto my iPod that I needed, not knowing about Archive and Install, but I did not have enough space. I deleted the music files of my iPod (G4) within iTunes, and put the files on there, because I didn't know if I could get them off that way or not. When I went to put the files on the renistalled Mac OS X 10.4, some files didn't play, some skipped, some ended and went to the next song, and some songs played clips other other songs in my library then ended. My purchased music does not play, and is messed up, along with the other files. My files outside of the music was fine, but something went very wrong when it came off or went on the iPod. Almost all the files are completely damaged, and I had many, many songs in my iTunes Library. I spent over $100 dollars in the iTunes Music Store, and downloaded the songs on another computer, and have been transferring songs like this for a long time, on both Windows XP and Mac OS X. This is the first time anything like this has happened to me, and because nothing ever went wrong on iTunes on Mac or Windows, I never made backups, as it would take a long time with the music I had, and not many people I communicate with mention that they do it, or do it. I don't know what happened this time when I copied the songs over to my iPod this time, but this time I know I reformatted it to a Mac format, not the one Windows XP formats it in, and had the original firmware. It may also have been because there were more files this time, more freeware applications that I did not want to redownload, text files, pictures, folders, and music than before, but I did not expect that to make any difference. I had returned a PPC Mac Mini because the Intel Mac Mini was released 14 days after we bought it and had it shipped to us, and used the iPod to transfer the files I had made/put on the PPC Mac Mini onto the Intel Mac Mini. I put my files on the PPC Mac Mini with my iPod, but because I had 400-500 less songs, I didn't have to delete the music off the iPod in iTunes. Because I thought nothing would go wrong, as it never had before, I used Erase & Install, instead of Archive & Install, which may have kept the now corrupted music files. The only files damaged were the song files, which are almost all damaged. I had copied the whole iTunes folder from my previous Mac Mini, and had the iTunes Library Data.xml, along with all the files. I copied the files from the iPod into the Music folder on the computer, and used the Library file. After opening it and changing files to see if it would fix my problem, it became damaged, and I didn't know what to do. I copied all my music from the iPod into the iTunes window, and it was still corrupted, this time losing my playlists. I did that process one more time, and then lost all Smart Playlists, wihch I used very often. I tried to test the files on a Windows PC, but it could not read the iPod, because it was formatted on a Mac. My older music is the things that are mostly affected, so my recently ripped music has less problems. I have no way of finding out what caused the problem and fixing it myself, so here is what I'm asking. I'm asking if there is a way to get my music back, from either a cache or something on my iPod, or from a file that was left on the harddrive during Erase & Install, fix the damaged files, test it on a Windows PC without having to erase the iPod, or in the very least replace the Purchased songs in iTunes. I looked in the Terms of Sale and it did not say anything about if your files were damaged, or something that was related to my situation enough for me to fix it. The things I want the most are all the songs back on a computer, not damaged, or at the very least a refund or replacement of purchased songs. I have Apple Care, and am proceeding to see what it can do to help me."

Answer 1

If the path to a file is too long for iTunes, you get this message. Unfortunately the limit of iTunes is less than allowed in Windows.
iTunes fix claims to be able to deal with this, but I haven't tried it myself:
http://itunesfix.com/iTunes%20Fix.html
http://itunesfix.com/iTunes%20Fix.html
(I am trying out two diffent ways of giving a link. Hopefully they will both point at the same place.)