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I dunno how feasable this idea is, but maybe you need to run all the mp3 files on the server through an mp3 renamer and then have it rewrite the filenames to some sort of standard. This does assume that the id3 tags are correct (probably not but you never know). i would think that if you had duplicate files it would show up as songname(1), songname(2), etc. and then you just need to look for the files with the (#) and delete.
Of course this is just an idea and I have NO clue how well this would work depending on the mp3 files, mp3 renaming program, etc.
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