How do I add a discount after an order has been fulfilled?

[jtaggartaz]

Because I can sometimes use a smaller box to ship an order of multiple products, the default shipping box and therefore cost is too much. However, I don't know by how much until the order is created (and I've already selected the shipping). Then when I go to print the shipping label I can select the actual box I used and adjust the weight if necessary, the cost of shipping changes (usually significantly less). I want to give the customer the additional savings/discount but if I've already fulfilled the order I can't adjust the invoice to the new amount. 

How can I adjust an invoice amount or give an additional discount that the customer can see after the order is fulfilled and before they pay the amount that is too much?