No they will not. the male may call to her but that's because she goes into heat immediately before, during and after birth. He's just trying to mate. they will be just fine apart. If you can sex the babies (there are pictures in a sticky in this section) you might be able to keep same sex kits (son with dad, mom with daughter) after they are weaned if you want them to have companionship.
Make sure you mark the date on the calendar 111 days from birth because there is a good chance she's pregnant again if he was in there when you found the babies.