how to process short shipped orders?

Here is a common scenario for our business can someone explain the best way to handle this in product cart.

A customer orders a product we do not have enough of. Let's say it is 100pcs we only have 98pcs. Typically we ship the 98pcs and the order is considered closed, We do not do back orders.  The customer has authorized the full amount, what I have been doing is editing that order so it reflects the actual amount we are shipping and then the total is correct and I can then capture the correct amount. I suppose that works well enough, however I just changed the order and there is no reflection on the invoice that the customer originally ordered a different quantity. That is confusing to them and us when looking back on it.  Any advice on how to handle this differently?

Thanks
Chris