The events of "The Stolen Earth"/"Journey's End" have been "unwritten" from history, probably by the same "pure time energy" that came out of the crack and erased the Clerics and the Weeping Angels in "Flesh and Stone".

Time travellers can still remember events that were unwritten, as long as they are not part of their own history, but no one else can. This is why Amy remembers the missing Clerics, while the remaining Clerics do not.

Since Amy wasn't a time traveller when the Dalek invasion was unwritten, she doesn't remember the Daleks.