I have a folder of MP3s, some of which date back to 1999, just a few years after the format was popularised. Most of them have utterly terrible names (think RIDEONAM.MP3). I think at this point they might even survive the heat death of the universe. And they’ll still be terribly-organised.
I have two directories. The original badly sorted one and the duplicate directory that I ran through some tagging software that failed to properly tag everything. Of course I was going to fix that and so I added things there that aren’t in the original directory so I have to keep both around.
Precisely this situation is what’s keeping me from just giving in and having the whole thing autotagged.
IIRC, filenames/tags aren’t included in a file checksum, only content, you could sort them that way to get rid of duplicates.