And even in filmed, televised and theatrically-released stories you often have debates about whether certain stories are even canon to begin with. TAS, for example. We still have debates about the official status of the animated series and the thing ceased production almost 40 years ago. I still know more than a few fans who don't include TAS in the history of Kirk's original five-year mission. Gene Roddenberry went to his grave saying that elements of Star Trek V
weren't canonical and he didn't accept them as part of the Trek timeline and backstory to his characters.
So yeah, canon is not only rewritten from time to time but it's also rejected by the very creators of the franchises themselves.