She's a time traveler, so she can remember versions of timelines that no longer exist, at least the ones she personally experienced or remembered hearing about. This is also why when Companions interact with history they can claim "but I don't remember it having happened this way!" - because they can remember the original timeline (or rather, its effect on their personal history, i.e. What they originally had to learn in history class because of the way things originally worked out) before alterations were made.
Anybody who travels in the TARDIS has this effect happen on their memory to some extent or another. Which gets REALLY confusing for Amy after time has been rewritten to include her mom and dad again, as she can suddenly remember both timelines at once, each coexisting, which seems impossible, but isn't, since of course, she's actually LIVED both of them, because she undid her parents being unwritten, thus changing her own personal timeline (normally a no-no, but I think the fact that it was all being UNwritten, and thus needed to be returned to its original, natural state, had something to do with all that).