No problems, i think it will require a new game but at least you won't have to worry about the loyalty problems any more.
Is this game really good enough to start over from the beginning just to solve loyalty problems or fix quest bugs? I've seen so many people in the forums say they've started over because of x and y but personally I just want to complete the game and put it away. I'm a big fan of the genre and have every similar game I can think of but this one is so bugged and unfocussed it's just not enough fun for me to want to do it again. If I started again it would be on the easiest setting with all the 'arcade' style gameplay options ticked and the debug menu as a permanent suppliment to the game. As it is I've had godmode enabled for the most part of playing this game as the level of combat difficulty and easy to fail quests just makes the game incredibly frustrating.
So much so that I don't think I'd ever restart it even on the easiest arcade settings unless I was doing so to play through one of the community made mods or plotlines on show here. Even before they're finished it's clear they've had a lot more time, effort and attention to detail put into them than CoAS which quite frankly isn't one game at all but several different storylines all thrown together without being completed, checked or even submitted to the laws of common sense. Usually when a game does badly it's because the designers wrote it badly or the developers coded it poorly but I think CoAS has actually managed to do both. Everything about it is standard at best with the majority being just plain poor. Throw in the fact that 90% of the game is a direct port of the previous title released how many years ago and they haven't even tried to better themselves.
I paid good money for this game so I'll be playing right through it and claiming completion but after that it'll be uninstalled and lost forever and quite honestly I have no idea why anyone would want to give this game a second chance unless they're playing with serious moddage. So you can patch it to fix one bug, what about the rest of them? Fact is this would be an 'acceptable' end result of an unfunded community project but when you look at it as a professional title they shouldn't have even released it. No wonder the companies responsible are going bust...
Don't restart, just get a better game!