~ Rewrite ~
Setsuna didn't want to be biologically related to Sara. The shard of Lucifer's soul housed within the Seven-Bladed Sword of Heaven did not want to return to his erstwhile home, nor to continue living out the human life of Sakuya Kira. Mr. Kira didn't want to lose his son, no matter how much of a delinquent or criminal his son had become. The real Sakuya didn't want his father to grieve for him.
Organic Angel Alexiel may not have had powers anywhere approaching those of the Antichrist child, but some of these wishes were within her purview. She used her astral powers to overwrite Setsuna's DNA to make him the biological son of Mr. Kira. She then overwrote the father's memories so that he remembered Setsuna as his son rather than Sakuya.
Adam Young's influence was needed to alter the rest of reality to match the changes Alexiel had made. Adam didn't think it was right for the sword and the soul shard and Sakuya to all remain in one body, but he did not try to force them apart after being told that they wished to remain as one being.
With 'Sakuya Kira' written out of existence, or at least falling beneath the notice of the rest of the world, Lucifer was free to walk the earth as he chose, without being tied to the life from which his current body had originated.
The most difficult change for Setsuna Kira was getting used to having a parent who loved him unconditionally, and one of the first things he did with his new lease on life was promise his new father that he would try to be less of a delinquent. Setsuna's hair was a darker brown now, due to the change in DNA, close enough to the color of Alexiel's hair that they could almost be mistaken for mother and child when standing next to one another. Which struck him as both ironic and somehow comforting.
For Sara Mudo, getting used to the idea that she did not have a brother anymore was easy enough. However, the retroactive changes to her family history meant that her parents had never divorced, and she had no reason to resent either of them. It was strange seeing her parents so in love with each other again, when she remembered them fighting bitterly anytime they'd been in the same room together for most of her childhood. She thought that gradually, over time, she would lose her memories of how the world used to be, but apparently she was too saturated by astral power from hosting an angel's soul within her body for that to happen. Her parents attributed her occasional bouts of brooding to her 'just being a teenager' and starting to have more adult worries. After 'meeting' Setsuna 'for the first time', her parents decidedly did not approve of her boyfriend.
Some things, it seemed, would never truly change.
~end~