I can't speak to any generalities but I have seen a number of different cases in different states and involving different versions of possession violations which also involved self-defense and I have never seen the relatively minor possession charge pursued.
For example, there was a case in NY where a woman shot an attacker with a handgun that she was not authorized to possess, as she did not have a permit of any kind, say nothing of that particular firearm being on her permit. However, the shooting was obviously righteous and no charges were brought.
I remember hearing or reading something from someone, I'm pretty sure it was Mas Ayoob, about the idea of Competing Harms. In this case, between getting shot because you couldn't defend yourself, or carrying a gun somewhere you're not supposed to, you probably won't be brought up on possession charges because obviously, being shot is a bigger harm than possessing illegally. Not every state has this, and handgunlaw.us doesn't go into it, so you might have to do some digging.
I'm pretty sure the person who said it, concluded with something like, "Think about how many times you've had to use your gun in self defense, compared to the number of times you've accidently flashed, or your gun printed, or something like that." Basically, you are far more likely to get a possession charge, than you are to have to use your gun in defense. So...do what your going to do at your own risk.
Wikipedia entry on this concept: