They really don't have to give dates as to when Khan ruled the Earth. He's an evil genetically engineered dictator from the Earth's past; that's about the extent of backstory we need (one doesn't even need to know he's Sikh, though you may as well).
Basically this is a huge nonissue and I suspect if O&K did put Khan in a movie they'd just sidestep this matter entirely, and they'd be right to.
So no, this isn't something that has to be retconned. Just ignored. The new films will be doing a lot of the latter - it's not likely to be visiting the planet where Apollo or Plato's stepchildren or gangsters or TV-watching Romans hang out, for obvious reasons, but in 'canon' these would still be there.
I quit watching ST:ENT during the Xindi arc ("We are evil lizard men bwah hah ha!! ... "
), though I heard that they introduced a ship full of Augments later on in the series. I'm curious how they handled the origin there. Did they re-write their origin, keep it vague and unexplained or just completly ignored it outright?