ShippingEasy integrates with FedEx to offer Multi-box shipping. Occasionally a shipment needs to be cancelled due to an order cancellation or other reasons. With FedEx Multi-box shipping, however, when one shipment needs to be cancelled within a group of shipments the entire group needs to be cancelled in order to get a refund for that shipment.
You have three boxes filled with products but only the products within two of the boxes are ready to go out. As the shipments are grouped together in a multi-box shipment, they are seen, in a way, as one shipment on an invoice. Because of this, you will need to cancel all three labels to get a refund for any labels you do not use. You can then recreate a shipment based on what is ready to go out.