Remember, the continuity back then was pretty loose. Yes, a number of the books had interconnections or cross-references, and that was starting to get more systematic in the last couple of years before the Richard Arnold crackdown on continuity, but it was never as tightly unified as it is today, and a lot of the books that were nominally in continuity with each other nonetheless had differences in detail and interpretation.
And like I said, there was never any explicit statement that there was a second 5-year mission. That's largely my own extrapolation that I made in the "Continuity of Days Gone By" thread, based on a fan theory I remember hearing about, in order to explain the occasional strange timing reference in some of the novels, like The Romulan Way
being 8 years after the third season yet somehow still pre-TMP. These are subtle timing discrepancies that readers -- and authors and editors -- back in the day could easily have overlooked.