Fenic's mother is not the lost Princess
Enae was an Unreliable Narrator, and it was the Princess with the yellow scarf who died, not the Princess with the blue scarf.- Careful observation of Enae's narration
shows that the Lost Princess' scarf's glyph doesn't match Fenic's. The woman with the blue scarf does. - Fenic's narration at the beginning of chapter 1 features the Princess with the blue scarf, and implies she had something to do with Partition, which would seem to contradict Enae's story.
- This also solves what would otherwise be a Plot Hole; Fenic's mother died, while the Lost Princess was said to be immortal by God.
- As for Fenic, well, eggs could always be preserved from a recently deceased corpse. This could go a long way to explaining Fenic's similarities to her mother, as she may have been engineered to be as close to her mother as possible. As for why she's transgender, well, maybe they thought a "boy" would be easier to control.
- Alternatively, she's a clone of her "mother", where something went wrong in the process or the DNA was damaged, possibly leaving Fenic with atypical chromosomes (such as an XX "male" or XO person). It's also possible her "mother" was transgender too.
- It's been 17 centuries and Enae almost certainly heard the story of the Great War second hand. It's possible that someone spread the lie that Fenic had been the Princess who escaped, potentially to protect the true Lost Princess from people searching for her.
