The 8u2 or 16u2 on mega and some custom uno are the serial converter uCs replacing the Ft232rl serial converter chip unlike 232 rl the 8u2 and 16u2 are uCs programme to do the Ft232rl work and they have protruding icsp headers which can be connected to reprogramme them, but I think as you dont even know about them then you won't have messed up with them.