Official comment

For starters, what did you do to wind up with multiples? Have you at some point moved the physical audio files and then imported them again.. twice? That's the only way that would happen. The reason you can't relocate the missing song is the fact the song living at that location you pointed to is already in the collection.
There is no surefire way to clean house, but my recommendation would be to figure out how/when you imported the duplicate tracks - sort by the location and/or the import date, then purge the new ones, leaving the old ones (which presumably also have more hot cue data?), then perform a mass relocation.