Mxyzptlk revealed that both the New Earth and Prime Earth Supermen were actually two halves of the true, complete Superman, who was split into two separate people during the Flashpoint incident. The same was true for Lois. Out of love for Jon, Clark and Lois merged with the essences of the other two and each became single, complete Prime Earth version; fixing their conflicting histories and bringing the world back to normal.
Current Version:
Superman (Genesis Enhancement)
Former Versions:
Superman (Reborn)
Superman (Parallax)