Continuity Confusion

I just watched the Voyager episode 11:59, which is a fluff episode focusing on the romance of Janeway's ancestor. It's set in the year 2000, the contemporary year of the episode aired, and all I could think while watching it was "So...uh...is this the world that's been wrecked by the Eugenics War?" Because TOS said that happened that happened in the 90s. Honestly even in TOS that was probably way too early to place such an event, of you think about it, Khan probably would have been already born the same year his episode aired, but, whatever, they didn't know they were making a classic that people would still be obsessing over half a century later. I would personally say that, even if the date was too soon in the future, once it's established you should stick to it. But, as I understand it they haven't. I think a young Kahn shows up in one of the more recent shows or something and the Eugenics Wars has been pushed forward. So I'm asking when is all that established (if I'm right). I don't think the intention of this Voyager was to show a world devestated by the Eugenics War with deep space sleeper ships existing. So is that an oversight or did supplementary materials already at this point establish any retcons to the lore?