Cash basis or accrual? If cash, delete the invoice since it never showed as income. If accrual you need to offset it with a payment or donor credit, that you post as an expense, thus satisfying the invoice by applying the credit to it.
You might want to consider issuing Estimates instead of Invoices for pledges unless you need to have donors pay from within the emailed invoice. Estimates are non posting but can be converted to Invoices in whole or in part, which takes care of someone who pledges an amount to be paid in installments
