In the last episode,
after Ayato, Quon and Reika/RahXephon re-tune the world and made it so the events involving the Mulian never happened.
Haruka seems to have memories of the events that occurred before the tuning. Does everyone retain their memories or is it just her because she was with Ayato?
There is no answer to your question provided in the canon. After the tuning of the world, we only see a very short scene (at the very end of the final episode) showing Quon as a baby. It's safe to say that she probably remembers nothing. Ayato and Haruka (offscreen mostly) discuss things that indicate they may have some awareness of what happened, but to what extent they may have retained memories of it is impossible to say. Nobody else is referenced, so it's anybody's guess as to what the rest of the world knows/thinks.
Sorry to be so inconclusive.
