I'm guessing that Trek novels are written to conform to the screen continuity of the time. And it's only through subsequent shows and movies that they lose their conformity. Brownie points for the book, and the later episode/movie that contradicted that story, and the plot point in question. The more recent the book, the more brownie points to be had. Gold Awards for books that were apocryphal at time of writing.
So, you want us to name things? Like, in Imzadi, Riker's middle name is "Thelonius" and a year later it's confirmed to be "Thomas" on screen?
The "Augments" episodes of ENTERPRISE gave the Eugenics Wars a much bigger body count than my novels on the subject. They also introduced the term "Augments" which appears nowhere in my books . . . C'est la vie.
At the time of writing? Or at the time of publication? For instance, K.W. Jeter's Bloodletter plot hinges on the engine buffers that had to be installed on ships before they entered the wormhole lest the ships damage the Prophets. Except that's a plot point from the series bible that never made it to air. Or some of the early Voyager novels that refer to the EMH as "Doctor Zimmermann," because the series bible said that the EMH would take on the name of his creator early on. More along the lines of what you're looking for, Dark Mirror was a perfectly fine 24th-century exploration of the Mirror Universe, until six months later when "Crossover" aired.
Also, wasn't there an episode of Deep Space Nine (where Bashir's genetic enhancements are revealed) that altered the date of the Eugenics Wars by a couple of hundred years? I had assumed it was because the show was airing in the 90's, when the Wars had supposedly taken place.
Kinda-sorta. The admiral at the end said Khan's day had been 300 years ago (i.e. the mid 21st century), but Ron Moore later admitted that he had just lifted that figure from TWOK and forgot to account for the time that had passed since then.
Actually, the figure given in both The Wrath of Khan and "Doctor Bashir, I Presume" was two hundred years ago. Which really doesn't make sense...
As stated, it wasn't a deliberate alteration, just an error. My personal fix is that the admiral who said the wars were 200 years before was confusing the Eugenics Wars with the Augment Crisis from Enterprise's fourth season. ENT made it pretty clear that the Eugenics Wars had happened generations before; I don't think they explicitly specified the 1990s, but their references required them to be in the early 21st century at latest.
In the Genesis Wave books nobody seemed to know what Genesis was, but in the Voyager episode The Omega Directive Janeway knew what Genesis was and who built it.
Phlox says that the Augments are examples of 20th-century genetic engineering as I recall. Which only tells us when they were created, but presumably the war couldn't have been too much later.