Wow I'm a bit ashamed that I never saw that folder in all my searching. Thanks, that seems to have fixed it. I had a distinct feeling I was missing something crucial

So I just opted into the 13.0 beta on Steam and before doing so I had added a mod folder and some mods that I re-added using the in-game mod manager. However, it seems like Factorio still thought the previous mods were still installed, although updating it seemed to have removed the mods folder I ...