If I have duplicates and delete them, I would like my playlists updated. This would be a simple text search/replace of the deleted file with it's duplicate in the playlist file. I guess if there were more duplicates than one and you kept multiple, just pick one.
That is my biggest problem with the program now. There is no ability to preserve your playlists. I hate deleting something in a playlist.
Also, I guess if a log file could be produced when deleting duplicated, I could write a script to update my playlists myself.