She smiles as he seems to grasp the concepts now. But it falls a bit as he asks his question.

"Time travel can be a curious thing. Even for me. When an event like this happens and then things are set right again, typically only those at the centre of the storm remember."

It had been that way at the end of the Year That Wasn't, when she and the Doctor rebooted the universe, and when the Doctor had changed how he ended the Time War. They were at the heart of those events, so they remember both time lines.