I thought the NX-01 was retired before being refit to Columbia Class specs in the novels?
Nope, she was retrofitted in the second Romulan War novel, taking her out of the fight for some time. The novel doesn't specify the refit she was given, but Doug confirmed it was the Columbia configuration when he released all the original CGI work he'd done. The model he rendered was meant to have been used in some official capacity but it never was, after season 5 was cancelled and the novels choose not to use it on the cover.
It's been followed up by a model kit and the Eaglemoss special showing her that way made from the render.
She was retired months later when the war ended and Starfleet decides her space frame has taken too much of a beating from 10 years of active duty and so many fights. What they don't say is if she was at least re-christened the USS Enterprise NCC-01 before they do.