After watching the episode again, I'm not only pretty sure it's a Dream Lord hacked emergency hologram controlling the TARDIS, but the reason Amy doesn't remember the Dalek invasion is because the Amy the Doctor picked up was after he, himself, was locked in the Pandorica. This season has basically been a big paradox, hence the cracks in the universe.
That doesn't quite work, because the Atraxi in that episode clearly had records of the Daleks (and a bunch of other invading aliens as well),
and of the Doctor.
But there's got to be
some sort of paradoxical, timey-wimey thing going in, I think...
That's the thing, though. The first episode had all kinds of oddities going on, particularly with the TARDIS itself. It seemed unable to unwilling to deliver the Doctor to the same place he left... not just once, but
twice. There very easily could have been some timey-wimey stuff going on while the TARDIS was trying to repair itself.
Besides, that's the Atraxi's knowledge. No one's suggesting the Dalek's vanished from history the moment the Doctor was imprisoned (if that were a possibility, they'd certainly never allow it). Nor is it necessary for the Doctor himself to have been removed from their memories; they were there to imprison him afterall, so they'd be savvy to the situation and fully aware of who and what he was even after the temporal changes that occurred.
Heck, we even know that time travelers and other enlightened species are able to resist the effects of changes to the timeline, and practically everyone who was there to imprison him was a time traveler. Though how they traveled there is anyone's guess -- probably the Dalek's contribution to the alliance.
But yeah, anyway, it's still easily explainable why the Atraxi were aware of the Doctor, the Daleks, and everything else while Amy wasn't. The Doctor's influence on Earth was significant. As far as we know, he's only ever had one encounter with the Atraxi, and it was over and done with in the blink of an eye. His imprisonment would have far less impact on them than it would Earth's inhabitants.
A really big question, though, is why isn't Earth destroyed/conquered/complete screwed up without the Doctor around? Sure, his presence and involvement lead to
some of those encounters he thwarted, but there were plenty that weren't his fault.