Outlier,
I may have found a way out of this mess. I used Mackeeper (which I downloaded) to scan my external hard drive for duplicates, and then simply removed the duplicates there. Then I wiped out everything from iTunes and started over from scratch. Finally, I pointed iTunes to the external hard drive through Preferences, and when the playlist repopulated, it showed only one file per song, as it should. So far, so good...
I hope you get it worked out soon.