Official comment
The only reason, and I'll say it again, the ONLY reason files ever get listed as "already exists in your collection" is if you import that same physical file a second time (even if it's been moved to a different folder). Somewhere in your process after moving the file, you re-added it to your collection.
The best solution for you would be to sort by location, remove all the files in the "new" location, then relocate all the "old" ones (which more likely have the hot cues and memory points stored on them).