Mod Files Not Loading

[wholemilkgaming]

I recently reinstalled Skyrim SE after a hiatus due to my modlist breaking with the last update. Now I'm having issues with all my mods across multiple games like Morrowind and KOTOR. The mods just won't show up, almost like they aren't being connected to my games themselves, but yet somehow Skyrim still won't load without the proper mods. I tried a fix I saw online, but now Vortex is telling me that changes were made on the disk and that all my mods have been deleted. I still have all the files on my pc, but I have no idea what to do. I originally thought it was Nexus not staging to the right game file, but now I'm not sure. I have a different, mod list on my computer for some reason from years ago and I'm not sure why its still there, so I have no idea what's going on.

Any tips or advice?