I read this trilogy of books some years ago (must be at least 5-6 years ago; perhaps as many as 10). Three children, two boys and a girl, who have been selectively bred over generations to express a magical power which is banned in the world. It's a kind of cult obsession within a small town that's part of an expansionist empire that I want to call 'the concord' (but Google makes me think that's wrong).
These children have their magic 'emerge' in early adolescence. One boy is the most powerful and shares his name with another magic user of ages past, but he's also arrogant and quite sociopathic.
This boy ends up raping his 'sister' (the girl of the three) and she gives birth to an even more adept son.
Eventually the empress (or equivalent) learns of these magic users but boldly decides to support them publicly in the hopes they can be useful in future wars for this empire. There's a militaristic religious sect violently opposed to this who has a female leader hell bent on destroying these magical abominations.
Rapist brother is outcast from the group and learns to somehow raise the dead to fight for him. He uses this power to ally with an enemy of the empire which causes a war which essentially breaks it. He's defeated at the end but at great cost. The surviving magical children decide to withdraw from the world as it's clearly not ready for them.
The rape is around the end of book one. The rise of the dead as a threat is around 2/3 of the way in book two, and I think book three is just the full on war and subsequently spiral of worsening events. (I think!) Slim chance the whole story was just two massive books, seemed very detailed at the time.
Driving me mad not being able to find them!