I just solved a problem on my own, but since it was rather alarming at the time, I'll post the problem and solution here.
I restarted my computer after de-syncing Onedrive (it was causing unrelated problems elsewhere) and suddenly I could not load any save games in BG:EE or BG2:EE. I had two different installs of each, a heavily modded install and a completely clean install, and I couln't load saves for either of them.
But I still had the original save folders, which I could view outside the game in Documents. They didn't get deleted; the game just doesn't see them
It turns out that, for some reason, restarting my computer changed the folders that my EE games were using as save folders. Instead of using the folder from Documents, it used a different "Documents" folder only accessible by going to C:, then Users, then a different username from the one I'd been using, and then the other "Documents" folder.
I found this new folder by starting a new game in BG2:EE, saving it as "test 43235" to create a save folder with that name, and then searching my computer for "test 43235" to find out where my game had put it. I then copied my other saves to that folder and I was able to load them normally.