I wonder if we will ever get an actual canon explanation of what happened during the cataclysm between Megaman's era to the X era? Personally I blame Wiley faking turning good(again) to steal the X blueprints to make Zero. And testing it out on a prototype first(only because Zero's creator said he'd never do such a thing) which caused massive havoc. Resulting in Megaman having to be upgraded to X. Leaving behind his old body to be turned into Quint. Doubt we'll ever see it. Since that would mean an end to classic Megaman games.
Knowing how Inafune has been trying to kill Megaman to made it a Zero franchise since SNES days, it would be reduced to "they died and got forgoten by history, while Zero will be remembered 1 million of years from now."