Re: What to do with these Pokemon.
No, it does not affect the baby, and no, they will not mess up your game, even if you'd kept them.
They have no corrupted data, the game isn't constantly looking for "right" and "wrong" data, think of it as a form that the game is reading, it's literally just stored as:
Met at level:
etc, like reading off a form. The game just reads it and doesn't question it. The only time the data is evaluated for "correctness" is when going on random Wi-Fi or importing to another game like PBR, or playing in an official tournament.
I hope this has helped alleviate any fears.