Sales Update (FINAL) R42800 is run with bad data selection and Batch is corrupted?

We had two instances of corrupt sales update batches this month IB Type - one due to the user running R42800 twice -- the 2nd time before the first one completed and both with the same data selection, and one whose data selection collided with another site's data selection. Both batches were out of balance and thus would not post (corrupted).

Since the Final run of R42800 closes the sales orders, how have other clients handled this situation? In our case unfortunately, they were both SI sales orders and so multiple companies were impacted and included close to a thousand sales orders.