1 source file on external drive - but duplicates of files in iTunes - help!

I recently moved all my music to an external HD and followed mac's intructions for the transfer w/o any probs. However, the HD died (dropped it) and everything was lost on the HD.
To solve this, I used a program called "Pod to Mac" in an effort to recover all my files (about 35 GB) from my iPod. Worked very well. All files are now back on a new external HD.
The issue I've encountered is that in iTunes, I now have two versions of each song. Both versions in iTunes refer to a single source file in my external HD ... so if I delete one file in iTunes, I delete the source file for the second copy of this file in iTunes, too.
This isn't a big problem, except iTunes now thinks that I have 70 GB worth of music (ie, 2 times 35 GB; even though I really only have 35 GB of music), which means I don't have enough memory in my iPod to sync all 70 GB.
How can I delete one version of the file in iTunes w/o messing with the source file on my external HD?
thanks.

You'll have to try to repair the drive on a PC.
How is it possible that iTunes can read the files?
Some things will still be readable when corruption occurs, the big problem is when writing occurs when there's corruption.

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