I'm assuming at six weeks these youngsters are weaned. I would remove the doe to a separate cage and keep both her and the youngsters in quarantine to protect the rest of the herd while you are trying to determine what the problem might be.
Monitor them during the next couple of weeks. Watch for lesions on the face as well as on the genitals. Rabbit syphilis is not transferable to humans so I think the meat should be fine. I don't think I would want to use medication on rabbits headed for freezer camp, but if the doe has or develops symptoms you would want to give her a full course of treatment before returning her to the general population and certainly before breeding her.
Rabbit syphilis is a possibility, but it is hard to tell from the photograph. I wouldn't want to jump to conclusions at this point. I would, however, want to be very careful about isolation protocols.