Neither. When I remove all the files from the mod folder (leaving the empty stock folders intact), ALL my previously save factions come back, and duplicates are the most recent version. Curiously, a .zip file that I put some factions in to send to a friend before we could do it on steam also comes back. If I simply delete factions one at a time, they stay away, but if the folders are ever all empty, everything comes back.

EDIT: Two factions are uploaded on Steam, the rest are all made in the editor.

I've tried both ways of deleting the factions, and as far as I know, I'm not using any backup service, although I'm using Windows 10, which has some odd 'features', so maybe that's one of them?

This kind of thing isn't happening for any of my other games, steam or not. At one point I even uninstalled the game, deleted the whole GC3 stuff in 'My Games', and then reinstalled - and everything, including the zip file, that had been in the GC3 documents directory reappeared when I started GC3. I mean, it's not making the game unplayable, and I can just simply not select the civs I don't want to use anymore, but it's driving my OCD nuts lol.

I originally subscribed to 200 factions for a 100 player game to only to discover that wouldn't work with an insane map, so I spent a few days in subscribing some at steam only to find out I couldn't get rid of them. We need an easy way to delete factions in mass, not all off the game.

I like galactic civilization 3

Try going to the Steam Settings, Cloud, and turn off "Enable Steam Cloud synchronization for applications that support it".  Then delete your factions, start a game, and see if they still come back.  If they do, then I'm wrong about how they are coming back, my apologies.  If not, then at least you know the source of the problem, even if you need to turn the setting back on for your other games.

Early versions of GC3 supported Steam Cloud synch, but at some point the developers turned it off.  I'm thinking that somehow your version still has it turned on.

I had the same problem with ships and races. I turned off steam cloud sync and it worked. So I guess its more of a Steam problem than a game problem.