In the beginning of the game it explains why she resets the timeline:
Sana is the mother of the hero, Anon not necessarily the father. Europa said that they first have to defeat the Demon lord, and THEN Sana can give birth to the hero. She says that it would be too dangerous to put the hero in such a dangerous world (with the demon lord around), so they need to defeat him first. That's the reason of the resets so far.
When Kuma knocked up Sana and Europa reset the timeline, she even said how much of a waste that was. Because the child born from Kuma and Sana (being Kuma a pretty strong and gifted warrior) would have been really strong. She resets because the child must be born after the demon lord is defeated, she doesn't give a shit about Anon not being the father. That's the point.