Killing Flynt is story related and cannot be missed. I found the most effective and easiest way to kill him is with a shotgun and circling around him constantly so he typically misses when he shots at you. Make sure you fight him an open space area where you can do this and not in a tight area where you'll hit walls or objects. Also, taking out the stray bandits who are around will also help minimize damage you take. If you find yourself overwhelmed with enemies, head to the top platform where you can avoid gunfire easier. You can pick off enemies from here and then head back down. If you find yourself overwhelmed up there as well, just drop down and circle back. Rinse and repeat.
Happy Hunting :)