This is what happened to me also! I went into TOB and saw that my alignment had dropped. I tried to use SK but for some reason it didn't work. I even tried to change some of the global stats back as if I hadn't taken the sword but it still wouldn't change. In the end I just went back to my last save in SOA before I kicked Jon's arse and changed it there. For some reason it worked, all I had to do was beat Jon a second time (took about 3 seconds) and go into TOB again as my usual lawful good self
