The Stop Collection field only prevents Outstanding Invoice reminder emails. It does not stop Auto-BillPay retry processing.
Why It Happens
Once an invoice is already created, retry processing is handled independently from the Recurring Invoice. If the invoice still has:
Invoice's Retry Date populated, and
Pending Auto Bill Pay = True,
the Invoice Process Batch can continue processing the scheduled retry charge.
Resolution
To prevent further retries on an existing invoice:
Clear the Invoice's Retry Date field.
Set Pending Auto Bill Pay to False.
These changes stop the invoice from being included in future Auto-BillPay retry processing.