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Everything that happened because of a crack in universe 2 wasn't reset. The effects are still there. Prisoner Zero still escaped to Earth (as evidenced by "A Good Man Goes to War"), and the angels are still gone and so on. That the cracks "never existed" is a misconception; they did exist, as shown by the fact that the Doctor who rebooted the universe interacted with the cracked universe when his timestream unwound. The cracks were still in existence until his rewind was over, at which point they simply sealed; they weren't erased from existence.

As for Rory, the Doctor stated that when he rebooted the universe, they would all wake up where they should be (on 26 Jun 2010), and Rory was a human at that time.