What about casting Stupefy while I have an empowered Mel, Newly Awakened?

The chosen unit will be given -2 [M], to a minimum of 1 [M]. If it was 2 [M], it will become 1 [M].

In the case of Stupefy, Mel, Newly Awakened replaces the event of Stupefy giving -1 [M] with it giving -2 [M] instead. However, a replacement effect that replaces an event modified by the game effect that generated that event will inherit any of those modifications. In this case, Stupefy modifies the “give -1 [M]” game action and thus event with “to a minimum of 1 [M].” The replaced event will inherit the same modification.