Yes, he went back twice - the first time he went back, (at the end of series 5, after he'd steered the Pandorica into the heart of the exploding TARDIS, to allow its restoration field to touch every point in space and time and reset the universe, and when his life was 'rewinding') she was asleep. He put her in her bed and told her to remember him, old and new at the same time, in the TARDIS, which was borrowed and very very blue, before he went into the crack in her wall to finally allow it to close and so disappeared from history.
At her wedding a mysterious woman left her a blank old blue book and walked past the window - River, and her diary, now blank because the Doctor had never existed. The diary and the memory of something old, something new, something borrowed, something blue, helped her to remember the Doctor and bring him back.
The second time, from the Doctor's point of view was after Amy and Rory had gone, but from Amy's point of view before she fell asleep.
In fact, if the universe wasn't actually reset until the last crack was closed (the one in Amy's room, which the Doctor went through) that meant that the Doctor's first visit didn't happen, so unless he went back to talk to Amelia again, she wouldn't remember him, so he had to really....