SOLVED. Member of the green skinned alien race dies, his soul is placed in the body of a human girl who can use both light and dark magic, which are normally incompatible. Sci-fi Fantasy YA (not set in earth) [s]

[Tom]

I read this book when I was teenager. It would have been sometime between 2004 and 2007. It was one of those weird science fiction/fantasy novels, a mix of the two. It was definitely a YA book, I don't remember the author, name of the series or any of the main characters beyond "Mother". I read it between 2004 and 2007 but it could have been published awhile before that. I can't remember the cover.

There was a balance between a light and dark magic, but the two were incompatible.

One of the main characters was a girl raised in a convent, who discovers shortly into the book that she can use both types of magic

Pretty sure there was a supernatural being called "Mother" who used light magic, and either her friend or sister was the headmistress of the convent, and used the dark magic.
It was an alien world. Pretty sure the invaders or ruling class (I'm fuzzy on that still), were green skinned humans or lizard people.

The priest or mage class was a shadowy organization who used biotech and nanotech implants to give them special powers (teleportation, invisibility, shapeshifting, control over certain elements, ect). One of them, one of the good ones, was locked into the physical form of a bird. A lot of their powers were connected to their cloaks they wore.

One of the other main characters (one of the green people), his friend raped a native girl, things happened, somehow the main guy ends up in her care, they become engaged.

Main dude dies, his spirit is put in the girl who can use both magics. Native girl recognizes his spirit in her body.

There might have been a nomadic desert people that she gets sent to, or that might be an entirely different book.

I remember a scene (this is actually what reminded me of the book, and the rest of the details followed), where the dark convent leader is interrogating one of the last remaining servants of the "Mother", and wants to know where to find her. She inserts a small, magic glass tube down the nun's throat, that would crack each time she lied. If she lied too much it would shatter in her throat. It might have actually been the main girl this happened to, because I remember the mother interceding right as the tube cracked, before her throat was shredded. The Mother froze time and pulled her out of there.

I only remember reading a single book, but I think it was part of a series. The way things ended definitely implied it. One of the main characters is captured by the priests and changed into one of them, given the biotech head implants and nanotech cloak/robes.

[Tom]

The Pearl Saga by Eric Van Lustbader. He abandoned it to work more on the Bourne series, a financially sound decision if disappointing.

[Rainbowheart]

The Ring of Five Dragons for the trackable link.