The empire army book is set after the SoC, but it is very much so marginalized. The only direct reference and proof of this I can think of off the top of my head is Volkmar's fluff and frenzy rule where it mentions him escaping Be'lekor's battle standard and killing 75,000 demons with just some chains, then coming back and being re-instated as the Grand Theogenist. Though the implication is now he is tainted by chaos and it adds a creepy cool little piece of irony to the fluff. If nothing else came out of SoC that did, a definitive change to the fluff.
Before SoC: 6th army book doesn't have volkmar as a playable character (his fluff is in the book though, mostly pertaining to Luther Huss), though he is an internet character. In the 6th ed. fluff his absence from the army list is justified by him being reclusive since he "senses the coming storm". He is portrayed in a venerating light and also shown to be in the favor of sigmar since he can feel the crowning of the everchosen, sense the SoC coming, and also Knows that Huss is the man who will find the champion of light (and pardoned him because of this despite his break from the church). The rest of the Cult of Sigmar at the time is implied to be corrupt since Huss had to leave the church to fight the corruption and his piety is beyond doubt. Since Volkmar pardons him he too is shown to be above the corruption which seems to stop with the arch lectors.
In WD coinciding with the HoC release: Then when volkmar feels archeon beginning to muster his army, he marches a large force to the chaos wastes to attempt to defeat archeon before he becomes too powerful. He rides north with his WA (the only one mind you, which is funny since it gets lost) and a large amount of knights of the blazing sun. He fights archeon in the troll country, but he is too powerful and kills volkmar in a challenge. (there is a WD battle report for this when the HoC army was released)
During SoC: Volkmar lies there in the tundra, his corpse frozen and forgotten until months later Belekor's army marches in the wake of archeon's. When he comes across the battlefield he finds all the well preserved frozen corpses still lying where they were slain, including Volkmar's. He uses the powers of chaos to reanimate Volkmar (which in itself implies he is tainted by it). He then chains volkmar to his battle standard and fills his minds with the secrets of chaos. All this forbidden knowledge clashes with his faith and a great internal battle erupts within Volkmar, for a man as pious as he is, this is the greatest torture and Belekor delights in it. At the gates of Middenheim Volkmar breaks free of his chains and is rescued by the forces of good and taken back into the city.
In the 7th empire AB: Volkmar is back after his ordeal and takes his seat back from the AL that replaced him, but now he has a tortured and ravaged mind, with the taint of chaos remaining. That is why he has frenzy now, though I don't know how he got is WA back unless Belekor brought it back for him, which is nice of the Lord of Shadows. So now the "Pope" of sigmar is potentially an agent of chaos, whether he knows it or not. A nice twist.
So the storm of chaos did in fact change some of the empire fluff forever. And that made it into 7th. Surely not as much as was promised back in 2004, but at least its something. Undeniable proof that it did exist, but in 7th ed some AB's are set before SoC, such as the HE one and the WoC, and some are set after, such as the empire one.
