As the title says, basically. I have a few backup files in my 'saves' folder of games in towns that I don't play anymore, so I've deleted those games in-game. But I'm not sure if it's safe to delete the backup folders because they might not just be the game I played but they might be the actual town? So are they? If I delete them, will the town disappear as an option for a new game?

In your Saves folder? Those are safe to delete. When you do a Save or a Save As but do not change the name of your game save, TS3 creates one backup file of your previous save by that name. Those are just spare saves with a different extension in the folder name, not anything having to do with world or content installations.

Thank you! I've been having a load of crap issues with my game today so didnt want to do anything to make it worse