I had the same problem while trying to defeat the specter in the tomb. Once inside I realized had no potions so I attempted to run away and get some more, however a skeleton killed me. I reloaded my save to find myself outside with the experience and items I had gained inside. Also the doors to every building in town had disappeared. I found that if I enter another underground area, save, and then exit again and save the doors reappeared. However now I find that the door to the tomb is locked and I have yet to kill the specter therefore I cannot progress in the storyline.
