[this post sat unfinished in a tab for most of the afternoon; Christopher
has already articulated some of what I had intended to say, but it doesn't seem worth it to rework my entire post. My apologies.]
Canon comes from the institution, not from the individual.
This. We all have personal continuities, but "canon," for better or for worse, is out of our hands.
It probably bears mentioning that we, as Star Trek fans, sometimes might place a little too much emphasis on what is and is not canon. Canon is simply an arbitrary decision made by folks at Paramount regarding what needs to respected (as in, not contradicted) when new Star Trek stories are made. And even then, canon is sometimes ignored because doing so makes a better story (or because it makes an easier story to do
Christopher gave great examples of canon being contradicted, clearly without the intention of explaining away inconsistencies. (The appearance of Klingons, Trills, Romulans, and Bajorans, as well as the uniforms of the Cardassians, the varying warp scales, the date of Human-Klingon first contact all spring to mind as other examples.)
And what is canon has changed some over time; I remember distinctly reading a few years ago on StarTrek.com that The Powers That Be had decided that TAS was to be considered canon, whereas before it had not. (Only making this connection now, but that decision might have been to allow ENT season 5 to feature the Kzinti.)
I mean, canon in-and-of-itself is a means to an end. Personally, my favorite Trek story at the moment is a work of fan fiction, not even an official work of fiction authorized by Paramount. But this non-authorized writer is a very skilled one who brings the characters from the TV show to life just as well as the TV writers did. To me, that makes it equally valid as a Star Trek story.
Regarding the OP's question: my personal hope is that, were the current "novel-primeverse," in a post-Destiny Typhon Pact-era, to be irreparably contradicted by a new addition to canon, I would hope that the licensing people would have a change of heart, allow the current novel continuity to continue on its own, perhaps with fewer books, and start a new continuity with the new material integrated into that. It might mean having to include a brief timeline at the beginning of each novel, just so that the reader knows which 'line they're in, but I doubt that would be a real problem.