This post is just my attempt to reconcile exactly how Emil's retrograde amnesia works. Why can't Naminé exist in every world?
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Throughout the course of the original game, Emil is trying to differentiate his own memories from those of Ratatosk. He often has visions triggered by certain items or people, or simply has nightmares/dreams associated with Ratatosk. Filling in that other half this time is Aster.
Everything just got way more complicated.
When Ratatosk sealed away Aster's memories, he did it without knowing that Aster's essence would remain and push on the new memories Emil had in subtle ways: nuances of his personality, a tendency to read fast... Emil didn't find anything strange, really. As Ratatosk regains his strength and his own memories, the seal on Aster is becoming undone.
And the person known as "Emil" is slowly falling apart, being a fabrication, of course. Though Emil claims he has memories, in actuality he only has the most important ones. Canon shows this when Marta asks him where he was two years ago, when the Great Tree went crazy and destroyed Palmacosta. Emil says he wasn't there... but he can't name where he was or what he was doing instead. He reassures himself and tries not to worry about it too hard. He also mentions later on that he has memories from his childhood, but even those can be tampered with. After all, childhoods tend to be vague and influenced or even confused with dreams or pictures seen in a photo album.
When Ratatosk combed the dead Emil for inspiration for his new persona he was only able to pick up the most important memories-- the ones near the surface. The most recent events in Emil's life, his parents' faces and names, his favorite things, and a few brief flashes of childhood. Just enough to be convincing. It's possible that Emil's whole wimpy personality was constructed to throw off anyone seeking to destroy Ratatosk before he could awaken properly. Things like Emil's stubbornness and growing optimism definitely belong to his sleeping personality.
Since this was done hastily, it's natural that there are gaps in his memory, something that will become more apparent the further Emil gets through his canon. Aster is a very strong-willed person, and he wants to remember. And Ratatosk is having enough trouble being in charge as it is. So in the end, it becomes a matter of who can "become" Emil first... This red-eyed, human-hating monster, or his victim?
While Emil will be devastated when he discovers just what the heck is going on inside of his own mind and body and soul, he will also eventually recharge, wake up, and become whole. After all, there's more at stake here than he ever realized... And two best friends, a half-elf and a human, are at the center of it.