Canon is never set in stone. A canon is an extended body of fictional works that purport to take place within a single consistent reality, but usually the consistency is imperfect at best. Any ongoing series is a work in progress, and its creator/s may decide that early ideas didn't work, discover a mistake that needs correcting, gloss over old, minor details to make a new story viable, or simply forget something established early in the series.
But what is undeniable is that the job of tie-in books is to tie in -- to follow the lead of the canon they're adapting. They're expected to stay consistent with the canon as it's currently or most recently defined. The kind of situation you describe, where new canon comes along and contradicts what's going on in Trek novels or comics, has happened many times in the past, and every time, the tie-ins have been required to drop what they were doing before and accommodate the new canonical material. Sometimes they can find ways to reconcile the two, as when DC Comics managed (more or less) to squeeze The Search for Spock and The Voyage Home into their comics continuity. More often they just drop the old book continuity in favor of the new canonical continuity, as with the depictions of Klingons and Romulans in '80s novels, which were dropped when TNG depicted them very differently.
Essentially, the onscreen material depicts what "really" happens in the universe (although sometimes it's contradicted by later onscreen material, in which case the newer "reality" takes precedence), and tie-ins are only stories that might have happened in the universe. If new canon reveals that things "really" happened differently, then the "might have been" becomes a "wasn't." And new books therefore have to reflect the new reality.
More likely, it would simply be that the book continuity that includes Dax pursuing the command track and the Typhon Pact arising would simply be stopped and replaced with a different continuity reflecting the new canon reality. It would become an "imaginary story," to use DC Comics' term. As I said, this has happened plenty of times before. It's the nature of tie-in fiction.
Quite possibly, it could be declared that the main book continuity took place in an alternate timeline. Maybe, if there were enough audience interest and if the higher-ups were willing, there could be continuations of it published under the Myriad Universes banner, though I have no idea how likely that is. But the main body of Trek tie-in fiction would have to conform to the new canon, because that's what tie-in fiction does.
Anything that is mentioned only in the comic is non-canonical and therefore not binding on the novels. The books have to acknowledge what's stated in the actual film -- that the supernova happened and Romulus was destroyed -- but the elaborations in Countdown, like any other tie-in material, are non-canonical and only represent a possible interpretation of events.
Countdown's depiction of the supernova is extremely problematical. For one thing, it claims that Hobus is one of the oldest stars in the galaxy. The kind of stars that go supernova are extremely large and short-lived, lasting only millions or hundreds of thousands of years. The oldest stars are the smallest, dimmest, coolest ones, which are incapable of going supernova.
Or a musical composition in the form of a round. Or a code of ecclesiastical laws established by a church council (the original meaning from which the literary meaning is derived by analogy). Or...
