Several people have asked how to send an invoice to a client that has already paid. This is how I would do it: Create the invoice. Then record a payment for the full amount against that invoice (you'll find the menu link running down the right hand side). Now the Amount Due at the bottom of your invoice should be zero, and the invoice will have a status of Closed.
And now send the invoice. Maybe add a little message in the textbox - when sending the invoice - to say that it has already been paid.