You could delete the invoice and do a journal entry in general ledger to adjust for the entry that will be created when you delete it.  If it's associated with a job or contract, a gl journal entry won't fix those. 

Another idea is do a negative invoice and use a phony job number or contract.  Still do a journal entry in general ledger to offset the entry that will be created.  Then pay the two invoices that will total out to zero being paid.