Duplicates, triplicates, etc, etc.

We had a virus that could only be resolved in wiping out everything. After it was cleaned, the technician that fixed it, dumped all of our files into one folder. After installing itunes again, my husband synched up the ipod to itunes, but itunes dumped everything into a different folder. So we now have versions in folder 1 (backup) AND folder 2 (after reinstalling). But when we go into itunes, in some cases there are THREE copies of a song. Two in folder 1 and one in folder 2. We found if we delete one copy of the song while in itunes from folder 1, the song no longer plays. Weird, one version seems to ve a windows media audio file and the other is a mpeg 4 file. I'm clueless how to get just the one version of the song that I need. Also, after reinstalling V8 of itunes, itunes on it's own did some kind of conversion that seemed to trigger this problem. Any help would be great before my husband puts a hammer through the computer! Thanks! Oh, I did see previous discussions on dupes and to run the script to remove them, but i'm a little gun-shy in blindly trusting this.

+Also, after reinstalling V8 of itunes, itunes on it's own did some kind of conversion that seemed to trigger this problem.+
Probably the "Copy files" checkbox was checked.
How to turn that off: http://docs.info.apple.com/article.html?artnum=61658
If you're gun-shy about running that script, there are 2 ideas I have for you.
1 - Clean up the duplicates on your hard drive's folder 1 and 2. Then simply create a new iTunes library (press & hold the shift key while itunes starts) add you music into the fresh library.
2 - In view options, make sure the "Date Added" box is checked. Now sort your itunes library by date added. Maybe that will give you a clearer idea of when duplicates were added, and you can shift-select a bunch of them at once to delete them by hand.

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