I've been reading the comments about Alicorn mythology being ruined in the MLP universe because of Flurry Heart. I have come to the conclusion people are overreacting and blowing this thing out of proportion.
- Princess Celestia: The birth of an Alicorn is something Equestria has never seen!
- Princess Luna: It is beyond even our understanding.
It did not come across as "They don't know about Alicorns being born" but seemed to be "They don't know how or why in Equestria there is an baby Alicorn."
For all we know, the two only meant that Equestria has never had an Alicorn birth because they thought it was impossible. The Sisters obviously predate Equestria, are natural Alicorns, and come from a far land. It makes sense that they would not know how an Alicorn is born naturally in Equestria.
Amy Keating Rogers' book, The Journal of the Two Sisters, was just as vague as Celestia's and Luna's response in the premiere. Star Swirl heard of these creatures and ask the Sisters to rule the new country after finding them. They age differently from the other three ponies, earned their cutie marks in what could be considered adulthood in their subject's eyes, and were technically foreigners in a new world that they were just starting to learn about. A land without their own kind and that had no magic they recognized. They could've watched many mixed marriages of Earth ponies, Pegasi, and Unicorns alike and seen no Alicorns being born as a result.
It can therefore be assumed that they believed since former a Pegasus, Princess Cadance, was not a natural Alicorn, so they thought the baby would be a Pegasus or a Unicorn at least. Cadance giving birth to one is mostly likely a surprising side effect. They did not expect such an event like The Crystalling - Part 1 to happen.
Nothing is ruined in my eyes. I think it opens a door into my own theories of the Sisters origins. They predate Equrstria, were surprised an Alicorn was born in Equestria, and come from a land outside Equestrian borders. I think after awhile this will all blow over like all other overreactions in the past.