My P&L detail shows two income items of $500 each, for a total of $1000.  The actual income total for the two items should be $500.
One line is for an invoice on 5/18 under Accounts Receivable.
The other is for a deposit on 5/24 as just a checking deposit.
The invoice was printed and emailed.
The deposit was received as a check. 
I updated the invoice to show it was paid, so the invoice now shows balance due = 0.
(I saved the invoice, closed it, and reopened it to make sure the invoice showed a payment)
However the income line item in the P&L still shows invoice / accounts receivable / $500.
The $500 checking deposit has gone through reconciliation, so I do not want to delete it.
What can I do to correct the P&L?

(Seems like the AR amount for the invoice should now be 0, since the invoice shows a payment has been made, however, I'm not sure if that's correct or how to reflect that in a transaction.)

Any guidance on this would be appreciated.