Shortly after we realized our second "buck" was pregnant we had to separate her from her hubby. Now every time we check on them the buck's on the floor outside her cage trying to groom her through the bars. He refuses us when we try to comfort him and makes unhappy little grunts that sound like a child fighting to hold in tears. What can we do to keep him happy until his mate has had her litter?
Rabbits bond very strongly, you are correct that the separation is very stressful for them both.
Have him neutered, and they can live happily together for the rest of their lives. There are significant concerns about keeping rabbits together that are not spayed or neutered for any length of time. See At what age can/should a baby rabbit (kit) be separated from its mother? & How fast do rabbits really breed?
There is also some concern about keeping rabbits together in difficult environments.