It depends, a ruling by the FDA regarding tolerable levels of OA in honey and comb opened the way for a exemption to the old label. Technically, the label is the law - if your package says you can use it with honey supers on - you can. Otherwise, the honey supers should not be left on the hive during vaporization. You can place a barrier between the honey supers and treatment boxes or simply remove the honey super for a few minutes. Within 15 minutes of removing all the seals, it should be safe to return your honey boxes to the hive.