The reveal that Aubrey is secretly the spirit of Sylvain has a lot of subtle build-up throughout the series:
Her ability to use magic intuitively instead of having to "ask" Sylvain to change, which Janelle makes clear is completely different from how magic functions for everyone else.
Alexandra's thoughts and memories being involuntarily shared with Aubrey. She is implied to believe that she is not a true interpreter because she has never been able to communicate with Sylvain, but the truth is that Sylvain was on earth the entire time.
The crystal was not stealing Aubrey's life force, it was trying to put the spirit of Sylvain back where she belonged.
Dani explicitly tells Aubrey that she "feels like home", which makes sense because Aubrey is literally her home.
Aubrey is shown to have the ability to empower and "feed" Sylvains simply by being around them. How much of her relationship with Dani was influenced by this? Is Dani even capable of consenting to someone with so much psychic influence over her?
