I've also noticed that my inventory idle replacer (which is a few loose files, no esp) isn't working; normally, the character will stand with her hands at her sides if unarmed (a "blank" animation). And finally, I'm using Smaller Elf Ears, which is just a bunch of meshes for the elf races to make their ears smaller. Except now, their ears are freakishly long again.
I have no idea what's causing this: I know it's not mod-related, because I tried deactivating everything and starting a new game. I tried reinstalling the files (which were still present) and using archive invalidation, but nothing works. Any ideas?