but if they did already fornicate is there any harm in putting him back in if the female is not pregnant??
Nope, no harm. Actually most breeders will rotate their males in with a female (or females) many times over the season and try to get them to lock up a half dozen times or so. The mating process actually stimulates them to ovulate, and either the retained sperm or a recent copulation will fertilize the eggs... or a combination of the two.