My take on things is that, post-"The Big Bang," most of the portions of Series Five set in the "present" -- the 1996 and 2008 portions of "The Eleventh Hour," the 2010 portions of "Flesh and Stone" and "The Vampires of Venice" -- never happened. They're like the Year That Never Was from "Last of the Time Lords" -- the characters remember them, but they've been erased from history. (Except for "The Lodger," which I think now happened in a modified form, without the Time Crack appearing at the very end of it. 'Cos I like my happy endings for Craig and Sophie.)
However, I don't think this erasure extends to the portions of Series Five set at other points in history. I don't think the Time Cracks, post-"Big Bang," are still present in any of the stories set in other eras (such as "Flesh and Stone"), but I do suspect that their effects persist even without their presence, in the same way that the effects of Amy's parents' lives still persisted (i.e., Amy's continued existence, Amy's continued presence in the Pond house) even after they were erased from time. Cause-less effects.
And, for my money (since Moffat was kind enough to leave this up to individual interpretation), all the old alien invasions from the RTD era still happened, and Amy would now be able to remember the Daleks moving the Earth to the Medusa Cascade. And all of the RTD-era companions are just as we left them in "The End of Time, Part Two."