Reprogramming is not just for TMCC. Did you follow the manual instructions to reset the locomotive?
Sadly, when I've seen the smoke regulator forget the smoke settings, it's usually a bad regulator. I have seen the same symptoms, and it's always been a regulator replacement required. FWIW, the smoke heater on this model isn't affected by the R4LC as the smoke output of the R4LC isn't used, or is used for the cab light.
My Legacy system has been at the latest version since it came out, I've never had it cause this kind of issue with any locomotive.