>>123289357I actually thought about this a while back.
So David wants to train a perfect assassin out of his daughter. To do this he enlists the help of an organisation to provide resources, trainers and techniques. In post-Crisis this was the League of Assassins. In post-Flashpoint this was Mother. The first retcon would be that David was actually working for multiple organisations: promising them Cassandra when she was older, but in actuality he was just using them to further his own goals. One of these organisations would be Spyral.
So Cass' origin happens as usual. She kills Faizul at eight years old and runs away from David. For the next ten years Cass is homeless and David drinks himself silly every night. Then, around when Cass is 15/16, Mother finds her and captures her. They capture David too and tell him that payment is up and that Cass is old enough to kill for them now. David obviously knows Cass wont do this, but he also knows they'll kill her if she doesn't. To protect Cass, David uses the hypnos he learned from Spyral and changes/removes parts of her memory.
He changes the first kill from Faizul to Miranda Row. In reality David killed Miranda. He implants memories that make Mother's Organisation the only place she's ever known. David also knows that he has to traumatise Cass even more so that she'll appear "useless" to Mother as an assassin, so he implants false memories of David beheading and killed massive groups of people so Cass will be massively frightened of Mother. David succeeds in changing Cass' memories and works for Mother to protect Cass until he can find (or kill) a way out of this situation.
B&R Eternal happenes before he could do that, but he dies taking out Mother. Then the rest happens as we know it up until present day. Cass has an adventure where she fights the remnants of Spyral and undoes her false memories. We restore Cass' old origin, we restore old David Cain back and Harper can keep her origin with minor changes.