If this happens often, I'd create a custom transaction that will hold this AR (so you can separate it from your real invoices). And since the payment that comes in for a current invoice is short (due to an old invoice) and therefore you don't receive the full current payment, on the payment screen you'll want to fully pay off the current invoice but also add in the custom transaction would would be an offset. Therefore your total payment received in the bank is correct. Then, your custom transaction can show on AR reports.