You made invoices, for the Accrual Aspect? Then deleting them would be your error, of course. In Accrual Basis reporting, the date of the Charges matters to you. If that didn't matter, you would stop using invoice entirely; making them to delete them makes no sense. Just stop using them.
Otherwise, you seem to want to use recurring Invoices? You didn't state who initiates the ACH: you are them. I have 41 ACH invoices that are dated end of month, and I initiate the batch ACH around the 10th (Nov 13th, this time). In that example, the download banking has one lump value that I match to each of the 41 open invoices, to allocate that total ACH transaction.