It's said that this scroll can't be used on a beast who already has offspring. Does that include a male who has contributed to the fertility shrine/genetic program, but whose DNA hasn't been chosen yet? - since he could pop up in a Father slot somewhere in the future, and that might be weird for the database if he was now female...

Hello there! This question is in my mind too. xD

It little woried me. So I will watching this tread until the answer will be there! 

You can change the sex of a male who contributed his DNA but has no offsprings yet. After any female gets pregnant from him in any manner (through the shrine or naturally), it's not possible to change his sex anymore. So actually it's possible for a baby to have two mothers.

Wowie! Thank you!