Voiding single ACH payment in a batch - Invoice Cancellation

Hello All, 

The payment process request (PPR) we have submitted has made payments for 1000's of invoices. Since they are Electronic (ACH) payments, they do not have individual paper document number. 

 -Now, Can we void the payment for one of the invoice or should i void the entire payment or payment reference number ??

The final intent is to cancel an invoice after voiding the payment, without having any double accounting. Since the payment is within a huge payment batch, i am not sure how do we take care of other payments which are already executed and accounted. Appreciate your insights