It's really no big deal. In practice, it just means that continuity flows downhill from the original screen versions, not the other way around. The books and comics and games have to be consistent with the screen versions, but the screen versions are not obliged to worry about what happens in the books and comics and so on.
(Although sometimes you do get a bit of backwash where something from the books manages to get "canonized" in the films--as with Uhura's first name, which originated in the novels but did not become "canon" until it was finally used onscreen in the last movie.)
Hope this makes sense. Ultimately, it's all just made up anyway, so fretting about which stories are more "canon" than others is kind of like arguing about how many Organians can dance on the head of a pin. An interesting exercise, but essentially pointless.