You have to do that!!!! Thats the most fun of all, bees aren't angry for taking the honey--happy to clean up the super your replacing. They will GLADLY rebuild anything you inadvertently destroyed and fill it back up again for you to take off later--remember Bees LOVE to work. Actually is a survival imperitave so they believe, we beekeeper only manulipate them to do what they would do naturally, but to our advantage. Next harvest you remove the supers, the little ladies won't care--to much.