Why?
I was in the middle of sifting through and organizing my CC, erasing duplicates and whatnot when i suddenly noticed that something isn't actually duplicate in the spot where CCMagic stores content, but only existing as a single file. On my entire computer.
And yet CCMagic displays it twice, and i can move both instances independently of each other to different folders.

Worse still this has happened to all my s3p files as far as i can tell, so now i'm scared to do something wrong and lose the organizing i spent literal days on.

Both empty.

The only copy of the given file is in a backup folder outside of the Sims 3 folder.

And since i don't know which files are duplicates and which aren't i can't just delete them all either.
And i can't check which are duplicates, because they only show up twice in CCMagic.
And i can't get them to not show up, because they stay in place even after a rebuild.

Worse still there are more files in the CCMagic list than in any of the folders backup or content folder.

How in the heck is that possible?

Well i haven't managed to figure out what went wrong, but i DID figure out a workaround:

-Back up the CC Magic/Content/Sims3Packs folder
-If you delete the unsorted instance in the Default set in CCMagic, it deletes the actual file in the Content folder.
-BUT if you don't open the sorted sets where the sorted instances of those files are, the "file missing" tag apparently isn't updated for them after deletion.
-So when you put the files back from the backup, the SORTED instances can use that file, but the UNSORTED instances will be gone.

As for the issue with there being more files displayed unsorted than exist, that was due to *further* instance duplications, and after i tracked down most i just accepted potentially losing a couple of files and proceeded with the deletion of the unsorted instances.

]

No idea. What you did was what I was about to suggest.

While annoying and bewildering, is it actually a problem? Since the duplicates are not loaded, it shouldn't be detrimental to your game.

CCMagic has been acting up a bit with me too ever since I moved to Windows10 but this is a new one.

It would have been a massive problem.
I have 5GB of cc in s3ps. This was duplicated, and it could have been duplicated somewhere on the SSD, taking up 5GB of unnecessary space. The game wouldn't have loaded duplicates, but CCMagic would still have merged them, leading to another separate 5GB file. 10GB is not something i'd just like to throw away.

Also there was a hundred items less in what i saw than what was displayed as duplicates. Meaning that there could have been good CC hidden in there, which i would have deleted had i deleted the contents of the Default folder without checking.

But yeah luckily what i did resolved things.

Oh, I misunderstood. I assumed the files don't actually exist as duplicates. Thanks for claifying!