Up until the "modern era" of Trek, my understanding of canon is that the Eugenics War happened in the 1990s and was immediately followed by WW3. It seems like that has changed.
Picard season 2 took place in the 2020s, and there was no evidence of widespread devastation that would have taken place in a major war, although it could be argued that it wasn't shown to us on-screen. At the end of the series, we see a folder labeled "Project Kahn," hinting that either Kahn has yet to be born or that the season's "bad guy" is planning to continue Kahn's legacy.
In Strange New Worlds Season 2, Episode 3, the focus is on Kahn and how he affects the timeline. We see Kahn as a child, meaning the Eugenics War has yet to take place, even though the episode takes place in what is obviously 2020s or 2030s Toronto. Even more telling is that the Romulan spy says "This should have happened in 1993." Might have been 1992; still, early 1990s.
This leaves me with a few questions. If the Federation time-cops are so set on preserving the timeline, why did they allow the timeline to be altered to such a degree that the Eugenics War, a major event in Humanity's history, happened at least 30 years after it was supposed to. In addition, what event actually altered the timeline so that Kahn was born/created decades later than he should have been? As far as I remember, we haven't seen anything to show why this happened.
Since we now know from SNW that the Eugenics War happened some time after the 2020s, how does that fit into the timeline for Zefram Cochrane's first warp flight? Assuming the Eugenics War is still followed by WW3, that only leaves a max of 49 years between the start of 2 major conflicts and first contact with the Vulcans. In "First Contact," Cochrane and company assumed the Borg attack was from a hostile force on Earth. Perhaps WW3 was still in progress, and the events of 2069 were what ended the war?
On a side note, the destruction of a single ship spawned the Kelvin timeline. Since SNW shows us that events in Earth's history no longer match up with the timeline established in TOS, TNG, VOY, and DS9, does this mean that SNW (and possibly PIC) are also in a non-prime timeline?
Wasn't that how the books established the eugenics wars, that the augments were working behind the scenes and influencing things?
Novelverse author Greg Cox’s attempt, to ‘dance between the raindrops’ to explain away a major 1990s war in Trek canon that no one could see in real life, was quite inspired.
There were however still numerous unexplained inconsistencies.
Beyond the ‘how is it really a war if no one knows it’s happening?’ aspect, there has been an inconsistency ever since TNG’s premiere Encounter at Farpoint pushed the timing of World War III back to the latter half of the 21st century.
Given this shift was based in Roddenberry’s own direction, Akiva Goldsman has a strong point that the Great Bird wanted the Trek universe to always stay a possible one for current viewers. As it happens, we can attribute the biggest shift in the Prime timeline to Roddenberry. There seem to have been further tweaks, but moving Khan’s birth to a later time seems a direct corollary of Roddenberry’s fiat in 1987.
TOS is fairly clear that the Eugenics War was the precursor of WW3, but TNG implied they occurred more than a half apart unless the timing of Khan’s rule and the Eugenics War is pushed back. Not to mention the hand waving to explain how none of us noticed Khan ruling a large portion of the global population.
While many don’t remember, this apparent discontinuity was a reason some TOS fans argued in the late 1980s TNG wasn’t in the same continuity as TOS.
Then there are other discrepancies such the later development of the Warp Drive and all the other Berman-era episodes that implied a shifted timeline. Voyager’s findings of temporal interference in 1990s California and the development of computer technology seem to imply that the writers were working off a bible with a revised timeline all along.
Greg Cox himself finds the explanation of accumulating effects of intertemporal interference to be a better solution. You can find his view on this in the comment section under Di Candido’s review of the episode Tomorrow and Tomorrow and Tomorrow.
Another Trek author, Christopher L Bennett who wrote the Department of Temporal Investigations books, also weighed in positively on the episode. He attempted to figure out when the major perturbations in the Prime Universe’s river of time took place, with Encounter at Farpoint being the first major one.