Most large scale breeding setups tend to leave the males in with them, once weaned remove the young then they repeat the cycle.

If there is any issue with the male and the neonates, the male is disposed of and a new male is introduced after the young are weaned. Same is said of females that fight or kill off their young.

Large scale is easier to allow breeding issues, because you aren't counting on every offspring as necessary food for your collection.

I wish I had the space for a large scale breeding setup.