Big Bang 2.0 was supposed to restore the universe using atoms from the original universe which had been preserved inside the Pandorica before the TARDIS blew up (by transporting the Pandorica into the heart of the TARDIS explosion, they would provide its 'restoration field' with so much energy that it could use these atoms to restore the whole universe as it was). From the [transcript][1] of "The Big Bang":

> DOCTOR: The perfect prison. And inside it, perfectly preserved, a few
> billion atoms of the universe as it was. In theory, you could
> extrapolate the whole universe from a single one of them, like, like
> cloning a body from a single cell. And we've got the bumper family
> pack.

I don't think it's entirely clear, but my guess would be that the Pandorica would only restore the universe to the state it was in at the moment it had been sealed up (using things like minute dust particles which had gotten inside along with the Doctor, perhaps), in the previous episode "The Pandorica Opens". And in that episode the cracks had *already* erased Amy's parents, so without Amy using her special ability to fight against the memory-erasure caused by the cracks (due somehow to having lived in the room with the crack in the wall), it would just restore a universe where she had no parents.

Also see [this answer][2] to a related question, which speculates about how the cracks don't completely write people out of history, but instead leave some traces of their lives even though most people don't consciously remember them (though time travelers can be an exception to this, as established in 'Flesh and Stone' when Amy asks the Doctor how she can remember soldiers who were erased by the cracks).


  [1]: http://www.chakoteya.net/DoctorWho/31-13.htm
  [2]: http://scifi.stackexchange.com/a/66401/22250