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Everything that happened in series 5 still happened. It's just that the only people that remember it are the Doctor, Amy, Rory and River. For example, in "A Good Man Goes to War" the Eleventh Doctor is able to recall "sexy fish vampires" and Rory being killed, erased and eventually plastic. Rory also remembers being plastic and waiting 2,000 years for Amy.

It has never been explained on screen if the events of series five have been undone or if anything to do with the cracks has changed. For more information/discussion, see Forum:I'm confused about the big bang two. Did EVERYTHING get reset back to normal or are there still things that were not recovered from time and didn't happen. However, because of the nature of time travel, one can still remember alternate timelines so the Doctor's memories aren't proof of anything.