The biggest example I can think of a book being retconned would be Starfleet: Year One, which was written almost immediately before Enterprise aired. I know some of the ENT: Romulan War and Rise of the Federation books have tried to keep certain aspects of what the book presented though.
That's not a retcon, though. A retcon is where you say something was part of the continuity all along even though the audience didn't know it -- e.g.
First Contact retconning the Borg Queen into the events of "The Best of Both Worlds," or
Section 31: Cloak retconning Admiral Cartwright as a Section 31 member. This is just a book being overwritten by later canon, which is something that happened countless times during the years that TNG, DS9, VGR, and ENT were on the air.
And I haven't tried to keep anything from
Year One in
Rise of the Federation. I considered it at first, but I found that book's version of early Federation history to be completely irreconcilable with ENT canon. So I decided just to do my own thing that was completely distinct from it, so they could stand as two alternative conjectures. The only points of overlap I'm aware of are things that both works borrowed from canon, such as Bryce Shumar and the other
Essex crewmembers established in TNG: "Power Play."
Something about that set up (Orion females actually having 'mind control' over all males) has always bothered me since I saw "Bound", but I can't really say why.
Perhaps because it plays into old, sexist stereotypes about women's sexuality being the source of their power and making them a danger to men's self-control. Heck, the whole idea of irresistible Orion "animal women" from "The Cage" is a blatant example of that stereotype, a misogynistic trope that goes back to Circe and the Sirens in Greek myth, and that underlay the atrocities of the Salem witch trials. You can see that trope in a lot of Roddenberry's work. His failed
333 Montgomery Street lawyer-show pilot with DeForest Kelley opened with a voiceover narration talking overtly about how women were a dangerous, devious force that lured men to their doom. Ilia's irresistible Deltan sexuality in TMP was a milder iteration of the trope. There's also the Venus drug in "Mudd's Women," Nona in "A Private Little War," the succubus in the
Spectre pilot movie, etc.