In short, from what I have gathered from the hints this chapter gives, the federation or star alliance (or whatever they call themselves) just recently discovered a new material, namely those kind of crystals.
It is highly likely that the cause of the mind/soul transfer, and this world's talk about demons and such is directly related to this "new" material.
In all likelihood this planet has much higher amount of it (comparatively) than other colonies/inhabited systems.
We don't know their nature as of yet, whether they are metaphysical, magical things or if they can be explained via science, but we do know, for now, that they are capable of transformation, be it mental or physical.
Our main lead likely actually truly died, but her brain pattern was transferred into the girl's mind, rewriting and likely transforming the person's brain at a fundamental level.
Well, if the crystal material turns out to be true magic, then it likely was soul and mind transfer, but until then, I think we should assume her as more of a perfect copy of her previous self.