Ah, another canon debate. Canon, to me, is what the late Phillip K. Dick once said about reality. It's something that doesn't go away just because you stop believing in it. Having ones work superceded by events is something novelists and other writers simply have to deal with and not just in the Treklit field. In my personal opinion (and that of others I've seen commenting here) one of the best Trek novels ever
was "Federation", which was totally contradicted by the film "First Contact", one of the best films ever. Am I supposed to not enjoy one or the other because of those contradictions? Not at all.
As Whitman said: " Do I contradict myself? Very well, then I contradict myself, I am large, I contain multitudes
." As for the larger question here, I'm sure that some will attempt to reconcile contradictions, others will ignore them. But the final question will be, as it is always: "Have we got a good story here or not?" If the answer is yes, then that's enough.