GW novels were never good in the first place actually, they've always resembled bad fanfiction, contradicting established lore in crass ways so regardless of what GW says, I consider them non-canon. Feel free to ignore them.

The writing of the End Times isn't top notch unfortunately, you can tell it was rushed because they felt the urgent need to kill WHFB as quickly as possible. I mean they churned out the most gigantic expansion in the history of the game over the course of a year, and a few weeks later removed all the evidence it ever existed and half the models needed to play it from existence. That's hardly good business sense. Still I'm thankful it exists, they could simply have shut the game down and said, that's it folks, Chaos wins, game over. Just imagine this scenario!