Use Empty on an item (e.g. box, pallet, container) with other items that were combined in it. This only works if the original Combine step was done choosing "Temporarily."
Simply record the ID of the item you are emptying. Then click the "EMPTY ITEM" button.
Empty will disassociate the contained items from the containing item. Then actions performed on the containing item will no longer affect the items that had been contained in it.
A good practice, unless you are re-using a container ID, is to empty the containing item and then destroy it.