^Yeah, it was set in the fourth season (the text says 3 months after "The Way of the Warrior," though I think it works better placed later in the season), but the timeframes of Trek novels that came out during the series often lagged behind the show by a year or more, because of the long lead time in writing a book. So it's not out of the question that someone writing a book set in one season would have knowledge of events from the subsequent season, or would come across that knowledge during the writing process and work it into revisions. For instance, just to pick an example off the top of my head, Q-in-Law
is set between "Deja Q" and "Qpid," but was written after "Qpid" with knowledge of that episode's events -- in fact, the novel makes an attempt to justify Q's lines about Picard saving his life in his previous visit as being about itself instead of "Deja Q" (though I don't think it quite works).
And of course Bashir was genetically enhanced all along even if nobody knew it, so there's no reason a fourth-season book couldn't reference the fact in Bashir's own thoughts, say.