They could always just explain it in a crossover game. Have Original, X, Zero, ZXes, Legends, and even Battle Network, Starforce, and X Over cross over in a big celebration. They could do some time travel stuff, so it can be anywhere in the "future" that they want it to be. I mean, they keep doing crossover stuff in some mobile games, I don't see why they couldn't do it in a more polished console game. Without microtransactions (looks over at X Dive).
(That way we can ALSO get Volnutt off the moon. And maybe show some of the Elf Wars pre-Zero. And...maybe connect Battle Network to everything else, why not? Maybe Battle Network's Earth is a actually a planet that the Carbons from Legends created so all the Humans in the moon could be reborn AND none of the Carbons had to die. Both races get to live! It's like a Marvel Comics Counter-Earth situation, crazier things have happened!)
Plus, I don't know if explaining what happened would kill any of the franchises off or not. It's not like Mega Man games are usually known for the plot. You could even use a crossover game to excuse any future games. They changed the timeline, so all the game series are in their own timelines now. The Mega Man games no longer necessarily lead to X. X no longer necessarily leads to Zero. The timeline was always a little wonky, due to games releasing out of order anyway. Explain what WOULD have happened...then change it. Volnutt saves Rock from dying at Wily-virus Zero's hands or something. I feel like part of the reason Mega Man games are getting so rare is because almost everything is so locked-in to each other, they have no idea where to go with anything. So, let them free themselves from being connected to each other. Let them go anywhere and do anything.
On the other hand...Making Zero the new main villain for a few Classic Mega Man entries would probably sell like gangbusters. Tell me a "Zero Trilogy" of Mega Man 12-14 wouldn't get fans excited. Wily is kind of over-played at this point. Zero COULD be the villainous shot in the arm the franchise needs, story-wise.