Duplicates in iTunes Media Folder

Okay, so first a little background. I had to reformat my Mac awhile back due to an issue with some beta software. Now, my Mac is back to working again... but since I had to redownload everything from iTunes Match to keep from having to redo the match/upload process and restart all that. But now, my iTunes Media folder has at least two of every file. (It's on my External Hard Drive, so I didn't lose my music with the reformat) I did this because I have movies, TV shows, and other content that I could not download from iCloud.
My question doesn't necessary apply to just iTunes Match though, just the duplicates. My iTunes Library has one copy of each, although Finder has two or more. I would like to erase the duplicates without messing with the songs currently in my library from iTunes Match. I would prefer to not need to delete it all and redownlad my thousands of songs from iCloud again. It seems like there would be some way to do this, and I would really appreciate any help I could get.

You could try using Robert Jacobson's script itunes_remove_notfound, or install iTunes Folder Watch and set its option to check for dead tracks on startup, or you can make a set of Lost & Found Playlists and delete what is in lost, assuming you're certain there is nothing in there that you want to repair.
I've also got a script for cleaning real duplicates. The current version just ignores missing tracks but I'm contemplating an update which would safely eliminate the broken link while preserving ratings, play counts, playlist membership etc, assuming a live duplicate to merge this data to has been found.
tt2

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