Originally Posted by Fallen Guardian
Don't try to just delete the Modules folder outright, that contains modules needed for the regular game as well. The override is completely deletable, as far as issues with the main game go. Any mods will be completely shredded by a deletion of the override, however. Yet at this point I think deleting the override, reinstalling all your mods and then loading a save from before you got into that glitchy module would be your best bet.
I agree I wouldn't delete the folder......unless you uninstall, cuz im pretty sure last time I did the it has folder called "saves" or something like that. And I personal would uninstall (I wouldn't keep save files just cuz of the possible glitches of reloading them, and don't forget to go and delete the files left behind after the uninstall), reinstall, install kotor patch (witch actually I don't have and my kotor runs fine), install BOS:SR, install BOS:SR patch, play through and report back
Hope it works!!