Hello AJ,
When you run the BOP, system triggers the Queue to R/3 and after updating the Sales order there will be another queue that comes back to gATP system. So, when you changed the sales order perhaps the flag is being resetted and thus it gets deleted from the above mentioned table. Please stop the CIF queue in APO Inbound after your BOP run to see what info is carried back to gATP.
Also, another important point to be noted is - whenever you store some data in the said DB table, ensure to enhance the //KOMGO structure to make it consistent with SAP's processing.
Thanks & Best Regards,
Babu Kilari