^The refit seen in the Ships of the Line calendar is just conjectural, Doug Drexler's attempt to rework the design into something closer to what he would've preferred if he hadn't had to answer to the producers' requirements. There's no reason to assume that the books would include it, though of course they could if they chose to.
But if the book is ambiguous on that count, then you could certainly imagine it as the refitted version in your own mind.
And the ending of this book doesn't exactly set the fate of the ship in stone. Who knows when or why that refit happened. In fact, the ENT novels don't mention an NX class past Endeavor (NX-06) but IFM mentions Intrepid (NX-07).
So I imagine the NX line wasn't shut down permanently during the war, just until it made economical sense to start the line again. Perhaps after the war, the Daedaluses were retired again and the NX line restarted. Perhaps with more time, the NXs were refit just as the Constitutions and Mirandas would be in the next century.
In a similar vein, wasn't the "Ship of the Line" picture of the crashed Columbia published before Destiny was written?