I'm making an assumption here, that you've got all your iTunes Media backed up.
If that's not the case do so now so you're covered if things go sideways.
Now you have 2 things to do, one delete the corrupted iPod back up correctly.
In iTunes go to Edit>Preferences
Click Devices (your iPod is not connected for this).
You'll see Device backups and the one you want should show the serial number of your iPod when your pointer is over it.
Select it and click Delete Backup (Scroll down to that button.)
Scroll down further and click OK to close the Window.
That should take care of iTunes .
Now your iPod, you will have to do a full factory restore, eliminating everything on the iPod and then you will set it up from scratch.
If you don't do that you will simply be restoring the corrupt file/files that got you into this in the first place.
Here are Apple's instructions :
http://support.apple.com/kb/ht1414
Remember, no back up!