Partially Fulfilled Orders, Mass Partial Billing?

Our company has software that automatically fulfills orders when our warehouse reports the order has shipped. This automatic fulfillment puts some orders into the "Partially Fulfilled" status when the order contains (in addition to standard, in-stock items) drop-ship items, pre-order items, or items with inventory discrepancies between NetSuite and our warehouse. Up until a serious problem we had today, I was under the impression that checking the "Hide Unfulfilled Orders" box would hide these partially fulfilled orders on the Billing form. Due to some strange problem with one of our saved searches, we have now charged many of our customers