This just happened to me but I fixed it. What fixed it for me was:
make sure vortex was fully updated (maybe unecessary since I think vortex updating silently is what caused all this in the first place, but safe to be on latest version)
disable ALL mods and intentionally run game clean and vanilla once
re-enable mods a few at a time, running after enabling each set incase one of them was broken/breaking bg3
Turned out none of my mods had issues I just needed to "run clean" one time. Probably some cache/orphaned file issue after the vortex update. I hope this fixes your issues!