My understanding of the question is that the OP had included postage in the price of the item (as we all know that that is how "free postage" really works).

They feel that by sending all the items in one box, and not refunding the excess postage cost (included for each item individually), they would be cheating the buyer.

Unfortunately you can't actually send an invoice with a discount greater than any separately listed postage cost.

The easiest way would be to ask the buyer to pay the full amount, then give a refund of the excess - I'm not actually sure if the "postage discount" reason is available when no separate postage is paid, but there is an option labelled "other reason" or something similar, which should work.