Rory got rewritten to a non-automaton version. Although not directly addressed, the reasoning behind this is that when the Doctor flew the Pandorica into the exploding TARDIS to form a universe-wide restoration field (gobbledy-gook from the episode) everything that happened due to the cracks was reversed.
Basically the universe gets rewound to a point before the cracks, at which point Rory had been (and always had been) alive in a non-automaton form. This reversal was shown by Amy's parents re-appearing because, as the Doctor points out, they must have been stolen by the cracks.
As far as I can tell, they don't explain why Amy remembering the Doctor causes him to reappear.