Hens dont generally "throw out" any eggs. When one hen leaves to feed or drink, the other one is probably trying to steal her eggs. They should never be close enough to do that. The same eggs are probably nearest the front of the nest so they get thrown out when the other hen comes back and they...
A week is plenty of time for them to be together if he is as active as you said. Important things with incubators is to get the temperature consistant, measure it at top of eggs, not floor, and if you dont keep the humidity consistent and correct for what you are hatching, there will be...