I expect they'll respawn. I think the only permanant way to deal with it is pay your bounty. Or just stay out of Markarth. i've gotten a characte rto almost Level 61 without setting foot in the place. Or Falkreath either.
What you done to annoy them? I found if you hit them and then put your weapon away they sometimes just try and arrest you. Then you can pay them off or whatever.
Guards can get funky. I had to kill all the guards in Rorikstead and at the Western Watchtower at one point. So I ran over to the stables and punched someone. After that the guards were reset to accept my yeild. So just go find someone to punch so you can reset the guards and then they will accept your yeild.
to be honest - i'm not sure...i did finish the decipher quest and now i'm done with the dark brotherhood assassinate one...i'm suppose to meet someone in town to finish....does anyone know if i'm suppose to just go ahead and do the prison quest w/o losing all my stuff?
Also, if you've done the Forsworn Conspiracy quest, the guards will target you no matter what, with no bounty payable nad no means to serve your sentence. You have to do the follow-up quest.