After reading the book, I noticed a few changes to the story. I know there are probably more, but these are the ones i found.
These first two may not be retcons, but simply small bits of information that wasn't worth adding.
-The story where the orcs met with Velen to discuss why they were attacking wasn't mentioned. Basically Velen met with the orcs at Oshu'gun to discuss why they were attacking. The meeting ended abruptly when Velen informed the orcs that Oshu'gun was the ship they came in and that it was absorbing the spirits of the ancestors.
-The second was the siege of Telmor. Basically some Draenei saved young Orgrim and Durotan and took them to Telmor. The orcs learned of the cities location and how to disable its cloaking field later using it to siege the temple. In the book it was mentioned that they were rescued and brought to the city but it never mentioned the siege of it later.
-The last one I noticed, was how long the Alliance was on Draenor before the planet exploded. In the chronicles, it took only like a week or so. Before chronicles, it was assumed that they were there longer. Both the Expedition Armory and the town of Kirin'var would have had to be constructed before the planet blew up, because they had docks which means there were still oceans when they were built. Also, the armory was built, destroyed, and replaced with honor hold all before the planet blew up. Lastly, Ner'zul, in the chronicle, just randomly opened rifts to different planets all across draenor, but in the old cannon, they took time to build frames for all of these portals, and you can still find a few of them in outland.
Did you notice any other changes to the story? I'm sure I missed some because I am not an expert on lore from the RTS games.