Upgraded Vista to Windows 7, iTunes deletes all folders on my iPod Touch

Maybe I picked a bad option along the way, I dunno.

All apps were on my C: drive, which was backed up, but the files were neither restored nor re-introduced to iTunes when iTunes was installed under the new O/S (Windows 7, 64-bit).

All music was on another partition. I did not import that folder into iTunes before attempting a synch. Maybe that was a mistake.

I installed the 64-bit version of iTunes. I loaded a couple of apps from the app store. I synched.

I chose "manually manage" at some point, and every time it prompted me to either wipe out the iPod Touch or the computer, I told it to keep the stuff on the iPod Touch.

After many questions, it wiped all of the music from my iPod. I freaked. It gave me the option to "Apply" or "Revert". I reverted.

Then I manually re-imported all music. It took only 5% or so. So I had to check "Synch only checked music", and it worked. Music problem solved.

But it wasn't synching any new apps. So I browsed to the "Apps" tab under my iPod, and noticed that "Sync Apps" was unchecked. When I check it, it tells me it's gonna wipe out the iPod. Not only that, but apparently all of my folders are gone as well.

Is there a way to retain the folders?

Thanks.