Closing only one line on Sales order

 On Sales order I have two lines one with item x quantity say 5 another with item y with quantity 5.Item y is substitute for item x. Both the items are shippable and invoiceable.

So customer ordered for item X but we are supplying him item y, at same time we want to maintain the sales order with exact quantity of X that customer ordered (Canceling line with item x is out of question).

How can i ship line with item y while closing the line with item x. Please advise. I can have an identifier by which i can identify the lines uniquely.