I've altered Aerie and Anomen a bit with Shadowkeeper, and Anomen is CN. However, whenever he has the conflict with Aerie, it comes up and ends normally, then Aerie just randomly wanders around the map and won't go where I tell her. What can I do?

It's a known bug. I believe that the solution lies - as it so often does - at http://www.baldurdash.org ;)