Go into the game and meet Vilja with her default looks. You will see a message in the upper left corner about "Upgrade to ver 3). After approx 30-90 seconds, you will get a new message that the upgrade is complete. Check that her inventory is working - if you did disable all changes of her, it will work. Now you can save game, exit, enable the cosmetical changes and return to your game. Her inventory should work properly.