IPod Touch has been synced with another Library- can't lose any data!!

Okay so I have my iTunes Media Folder on an external drive to save some space on my Hard drive. This just works fine, but yesterday I accidentally messed up my Media folder. Luckily, I got all my music, videos, apps etc back in original form, however when I wanted to sync my iPod Touch with My iTunes, I got a message saying that my iPod touch could only be used with one library and that I'd have to erase it! I have LOTS of app data and saved games (over 300 apps)... so is there any way I can make it sync without erasing? Help is appreciated!

Apps are not an issue since you can always redownload them for no additional cost if you are signed into the same iTunes account that purchased them originally. You can also transfer iTunes purchases to the computer. See:
http://support.apple.com/kb/HT2519 (redownload)
http://support.apple.com/kb/HT1848 (transfer)
It appears that iTunes now sees the fixed media library as new library. Is the computer authorized for the iTunes account on the iPod (Go to the Store tab in iTunes). On your computer if you go to iTunes>Preferences>Devices do you see a backup for your iPod? With you iPod connected to your computer if you right click on on your iPod under devices do you have an option to backup your iPod.
If you can backup your iPod and transfer purchases then you can restore the iPod using the backup and then sync. If You can't backup but have the backup already then you may be able to restore from backup. If you can't make a backup and one does not exist I know of no way not to lose yur data saved in your app.

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