I wouldn't suspect that an OTA update would reboot your truck, so to speak, and then clear your codes. It certainly could but that sounds sketchy. "Bad wiring" also sounds like a sketchy answer to you. Was that from the dealer?? I would suspect that the codes will show up again after 15-20...
I'm not a fan of levelling lifts because once you put some weight in the back then "your headlights are looking for aliens". I'd maybe go with a 1" or 2" regular lift. Keep the same factory rake.
YMMV