But thats why I say it would shake things up.
If he was wiped out and only got brought back once Amy remembered him, then it would have changed things around her in a big way.

As was noted when her mum first woke her up, she was surprised to see her, but couldnt work out why.
It was exactly the same thing that was happening to her with Rory, she kept crying but didnt know why.

Due to the whole trap being based on her mind imprint, she obviously became the key to reality (or sorts), so the only thing I could make a guess at is that the universe restructured still based on all the good the Doctor had done over the years, because there was still a phantom of him floating around in Amys brain.