THE EU was canon up until Filoni Clone Wars. It obviously had to be struck from canon when the lore between Clone Wars and the EU were at odds and Filoni regarded it as fanfiction. And if George was to ever make his sequels it would have been erased anyway. Even Zahn and KJA knew this in the 1990s.
Lucas was far more involved with TCW than he’d been with any prior EU material. Laying the blame for those contradictions solely at Filoni’s feet seems unfair - comments made by him, Pablo Hidalgo, etc. and the BTS material generally give the impression that they were at least trying to reconcile the new content with the existing continuity, whereas GL just wasn’t bothered.