Or simply that an existing earlier hypothesis was incorrect... like em.. science.
Right. Just because the characters thought timelines were changing in a certain way, that doesn't mean they weren't misinterpreting it. Maybe when they thought the timeline was being rewritten around them, they were simply jumping between two coexisting timelines.
Granted, there are enough "changing history" stories in Trek that in DTI, I had to acknowledge it as something that actually happened -- but as I explained above, it would logically have to be the exception, not the rule. The norm would be for parallel timelines to coexist, and specific conditions would have to be met for one timeline to come to an end. (Although its events would not be "erased," since if something happens, it happens. Those events just wouldn't be remembered after the two parallel timelines converged into one.)
But another thing I tried to get across in both my DTI novels was that the Federation's understanding of temporal theory was evolving and improving over time, so that by the 2380s, they had a firmer understanding of just what would happen in what situation. Implicitly, this is why Spock Prime wasn't worried about his timeline being "erased" when he fell through the black hole. By 2387, he understood temporal theory well enough to see that what happened to him wasn't the kind of event that would endanger his timeline. Any conflict between that and his ideas and explanations about time travel in earlier stories would simply be a consequence of his understanding of temporal physics improving in the interim.