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.
IIRC, filenames/tags aren’t included in a file checksum, only content, you could sort them that way to get rid of duplicates.
Precisely this situation is what’s keeping me from just giving in and having the whole thing autotagged.