My recollection is that the EU had varying "levels" of canon. So, the films were obviously canon, as were their adaptations (e.g. novel, radio drama, comic book renditions, etc.), with the films being the "primary" version. The licensed novels were considered to be cabable of being overridden by Lucas at any time, if he decided to chuck 'em. And then there were things like video games and the Star Wars RPG, which were NOT treated as canon, except for The Force Unleashed 1 and 2, which were treated as canon for marketing purposes, and then subsequently ditched by Disney (and a good thing, too).
Ultimately, it was all a little convoluted and I'm glad the Disney story group decided to ditch everything by default, unless they explicitly incorporate it.