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Goddess Madoka eventually cleaned up this entire mess after everyone died.

The Drakengard dimensional impact and the resulting magic salination and the "Gestalt" solution/Shade/Black Script situation caused a spiritual clusterkerfark of epic proportions. Fortunately the spiritual corruption was similar enough to going Witch that Goddess Madoka was able to guide them to a stable afterlife. Nier's Ret-Gone of himself to save Kaine got her attention. In fact, he's one of Madoka's rare male helpers.

• We do see Nier Prime and Yonah Prime together with the dead Shades in New Game+. Some deity helped. Since it's a Cavia world, multiple deities may have been needed for this one. And no, not the people eating monster babies.
• Nah, Cavia' world is too messed up even for Goddess!Madoka.

The reason there is Papa Nier and Brother Nier Alternate Universe is because of the Ret-Gone.

At first the universe tried to replace Nier with a different Nier, but then they made the same decision.

After ending D, the characters will find a way to remember Nier.

The nature of Nier's self-Ret-Gone isn't made entirely clear, but we know that he has indeed left traces of himself behind - Yonah herself couldn't really exist if Nier never existed (what with him being her father) and Kaine still gets to keep her Lunar Tear, and even remembers that it holds some sort of significance to her.

Furthermore, Yonah kept a diary which frequently mentions her father, and at least one entry explicitly mentions that her father knew Kaine, so the two of them can draw the conclusion that this hole in their memories is probably related to Yonah's father. Of course, this assumes that the diary remains intact, but even without it the fact that Kaine came to rescue Yonah ought to make them both aware that they are linked somehow.

Adding Emil into the mix makes it even more likely that they'll be able to piece some things together. Nier was instrumental in Emil's transformation, and his butler sent that letter to Nier before then - so without the memory of Nier, he will too need to search for an explanation for how those things came to pass. Since he clearly remembers Kaine and is trying to meet up with her, this reinforces the notion that they might go on a quest to figure out what happened to their memories.

And finally, there's all the villagers. Nier ended up affecting the lives of just about everybody in the game through his actions, especially via the sidequests. A lot of people are going to suddenly forget who it was that got them the parts to fix this or grow that or forge the other.

At the very least, I think that Kaine and Emil (and possibly Yonah, depending on how healthy she is) will go on a quest for answers, and considering what an impact Nier had on the world, I would be surprised if they couldn't find at least a few. Perhaps their memories alone won't be enough to call him back (this IS a Cavia game, after all), but I nonetheless think that Nier's Ret-Gone is not as final as it appears.

(addendum: This was written with Father Nier in mind. While some of the finer details may or may not apply to Brother Nier, the overall idea should work for him as well.)