are they even paying attention to the books any more becuase if they aren't please tell them to continue to not
They pay attention to the books, but they aren't bound by them. For instance, when the books came along and eliminated the Borg after Cryptic had spent thousands of hours developing Borg content across the entire span of the game, they didn't strip it all out. They just put a reference in "The Needs of the Many" implying it happened in another timeline.

The same guy at CBS who approves the books approves Cryptic's stuff. Cryptic uses book stuff that makes sense in their universe, and doesn't use the stuff that doesn't make sense in their universe. Since neither is canon, there's no conflict.
Unless you're He Who's Name Must Not Be Spoken, and he gave up after Enterprise. *cough*JD*cough*