Wow thats a tough one but the best i can think of is to go to your iTunes library then search for the song all the duplicates should come up the click on the top one the(while holding down shift) then click on the bottom one (they all should be highlighted now) then click delete.
Hope that helps/works
Manual seems to be the only way to do it, but if you go to itunes and choose duplicates, it will dupliate everything then its easier to delete the duplicates.