Honestly, I'm not sure anybody actually involved in the production really thinks about "canon" all that much. "Canon" is a fannish obsession. In all the years, I've been dealing with media tie-ins and licensed properties, I don't think I've ever discussed "canon" with anybody on any show. The word "canon" appears in no publishing contract or licensing agreement I've ever laid eyes on. It's only when talking to fans at conventions or online that the topic ever comes up.
On a practical level, it's simply a matter of treating the original screen versions as the primary source--and assuming that the screen versions automatically trump the tie-ins when it comes to matters of continuity.