Which is to say the extended universe of comics and books will be ignored if developer Black Tusk decide to re-write the series's history. The deciding factor will be whether it's 'fun' or not.
Studio Manager Rod Fergusson talked about this, multiplayer, fan feedback and plenty of other stuff in a Twitch livecast (and picked out by IGN), stressing that the developer was only 100 days into the new project which was currently in the "concept and prototyping" stage. However when asked about the story established in previous books and graphic novels he had this to say:
"Yes, as best we can. I believe fun is greater than canon. That's not to say I'm going out of my way to destroy canon, but if I get to a situation that may invalidate a comic book or a book, I'm going to make that fun decision."