This was my theory also, but it didn't quite explain her body's disappearance, as they said they've been looking for her, meaning the soul swap isn't entirely accurate.
I think the blonde prince, or maybe a third party, possibly took her with black magic and used black magic to alter her face and memories. Which is why he forbade her from the temple, because he feared that she would get suspicious if she learned black magic was performed on her.
cont...) like you said
it might seem crazy what im about to say
So my theory is that her soul was sent into the other body with black magic, and that's why her original body was asleep. Then more black magic came, and now she's back in her own body. And the prince seems to know her, which is why he kept her away from the temple and isn't surprised by the World Tree. I'm curious to see what happens next.