If they are well nuts, the rubber expansion nuts they use, the center will sometimes seize on the bolt and turn with it. If you can get something in there to squeeze it you can usually get the bolt out. Never use loctite on these because of this. If anything, put some anti seize on it.
Quick comment on this, as it also happened to me. The cowl bolt goes into a plastic plug on the seat, with a brass threaded insert. In my case, the issue was the brass insert spinning inside the plastic plug. I was able to remove the plug from the seat (with the cowl attached to it), but even then I could not prevent the brass insert from spinning. I ended up ordering a new plug (I believe it was $15 or so) and cutting the old one with the Dremel, so I could grab the brass insert with plies and loosen the cowl bolt.