Kenny came back at the end of the Christmas episode. After the boys and Jesus rescue Santa from the Iraqis (and Jesus takes a bullet for Santa, dying as a sacrifice to save Christmas), Santa addresses all of South Park and tells them that thanks to Jesus's sacrifice, he was able to make it out of Iraq, so from now on, Christmas should be a day to remember that brave man, Jesus. The town applauds, and then Kenny comes up to Stan, Kyle, and Cartman.
They casually say, "Oh, hey Kenny."
Kenny replies with a muffled hi. End of episode.