my understanding is that they can mutate...once they've infected a system. So while flawed code (like the Pulse) could initially infect a human being and "wipe the brain" (:rolleyes), it would mutate after infection. In other words, the Pulse itself would not mutate once it begins transmitting. It would not be unlike your copy of Microsoft Office CD spontaneously becoming the National Geographic library. Having said that, granted, I don't know how the Pulse was designed or how it works, and since it's fictional, I suppose a little dramatic license is in order and it can do whatever the hell it pleases. :shrug
But to answer your question about what happened to Clay's son: I think Pulsing him a second time wouldn't do a damn thing. It's like trying to return your computer to a former working state after it's been infected by a virus...by uploading a slightly modified version of the virus code.