There was a time a few decades ago when I tried to rewrite older books in my head to force them to fit with later shows and movies, but then I realized that by doing so, I was stripping them of the elements that gave them their distinct character, and that did them an injustice. They deserved to be appreciated for what they were meant to be.
Trek continuity is a moving target, an evolving process. Older books that fit the assumptions of an earlier version of the continuity are part of its history, a reflection of the form it took at the time, and that's worth preserving. Which doesn't mean that it's wrong to change it or to do new shows and movies in a different way. It's not a competition, and there is no "right" or "wrong" version of things that are purely imaginary. The older and newer stories are steps in an ongoing process of creative evolution. They are all "right" for their own place within the sequence. Altering things to force them into conformity would be like rewriting history -- or like creationism, denying the reality that things have evolved over time and still are evolving.