Hi!
I have same kind of problem. But it does not to seem be Nexus related.
My symptoms are exactly the same as you but I did not have Nexus installed when they started yesterday. I tried every advice I could google up. I updated everything I could think of. I did extensive deleting and reinstalling files and caches. Nothing worked. Then I tried starting to use Nexus. That did nothing. I reinstalled the whole game. That did nothing either.
According to everything I've read and tried myself the problem (or the visible parts of the problems) seems to be the file BG3 reads when running the mods: modsettings.lsx
As I've understood it, that should be the file bg3 reads what mods to implement. But starting yesterday, instead of reading it the game rewrites it to empty and THEN reads it. So the effect is no mods are loaded because there is nothing on that file to read. Why this happens could be some kind of concurrency file handling problem but that remains for Larian to figure it out.
If not that and someone has a better guess what to do please advice!