JMO but i think if you enter two deer then kill a bigger one then to bad so sad. However if you wait until your all done hunting, then you should be able to enter the deer.

Example, you shoot a doe and large buck during bow season and immediately enter it into the contest, your locked in. On the contrary if you get a doe and a buck during bowseason, you decide to NOT enter it automatically and get a larger buck during rifle season, you should be able to enter the bigger buck and the doe. Wait until your completely finished hunting to enter deer.