I heard from another player that breeding kills the parents. I think that's a horrid idea, but I know its for balancing and whatnot. There's a better way to handle that.
Here are some suggestions.
1. Put pokemon on a cooldown after breeding. Id say about a week is good but nothing like a month.
2. Make it so pokemon can only have a certain amount of eggs- but dont *kill them*. Like maybe 5 eggs per pokemon until theyre infertile?
3. Maybe give them clutches? you can keep the pokemon only being able to be bred one time and just give the person like 3-5 eggs. Still, don't kill them please.
4. So like, do anything that doesnt involve getting rid of the pokemon you bred. [Also being able to breed gift pokemon would be nice]
I'm actually a student game designer and digital artist and honestly, killing off the pokemon just seems like bad game design.