I'm not at home, so can't check my copy, but I've read the Gillen X-Men omnibus part two recently and I'd swear that either in the last chapter of his Uncanny or first chapter of AvX: Consequences, Cap tells Scott that Hope managed to fix the damage Dark Phoenix! Cyke did. The way I understood it she restored everyone he killed except for Xavier. Otherwise some huge cities on Earth 616 would be pretty much without a population after AvX?
In that case it's strange that she wasn't able to restore Xavier as well, but technically that could be explained by the fact that it wasn't Dark Phoenix but only Phoenix!Scott who killed Xavier?