Unfortunately, the theme GW has going in both Warhammer universes means that the result of a massive campaign like Storm of Chaos should be a minor or negligible victory for the bad guys. That's probably the main reason why the Eye of Terror campaign hasn't been retconned yet and SoC has.Wow, I just caught up with all that.
I'm kinda bummed about the retcon of the storm of chaos because there where some interesting things that came out of it. (what of Be'Lakor now ?).
On the positive side, Valten apparently gets new rules in the Nagash campaign book that Games-Workshop just released, so they are keeping at least a few good concepts from that whole thing. I would also be fine with seeing Be'Lakor go if it means the Skaven nuke disappears down the memory hole as well.