I don't think this will matter. It may if you are using the dining plan. That should be taken care of before you arrive. In any event surely they would fix that when you arrive, if necessary.
Other than that...when we did online check-in the kids room keys automatically didn't have charging privileges. I wanted them to, so they fixed that quickly when we arrived. As your DS is 2, you probably don't even give them a room key so you can just ask them to destroy the one they issue....I can't remember what we did when our kids were that young....