I reported the same bug. It should be fixed by the patch. However, if you saved your game the patch will only fix future play through : you will have to send a mail to larian with your savegame so that they can fix it for you.
I think it depends on the exact nature of the bug: the Broken Valley bug that involved the new and old versions overlapping doesn't seem to need the savegame to be fixed, but anything where characters etc have disappeared seems to need Larian to take a closer look. I guess the best bet is to try it and see before going for the more inconvenient option!
