Order Sync Flows issues Realtime and Scheduled creating duplicate orders

Here is the scenario: Realtime order sync used to miss some order syncs and we were unable to detect from Shopify end. The reason being the Shopify orders were synced with SO number from NetSuite. We would not know about this until the Customer opened a support ticket enquiring about the product shipment. So the solution was to enable the scheduled order sync flow so that this would pickup all the Shopify orders and ignore the ones already created and create the missed ones. This solution is working well, however we had further issues during the high velocity order times. Due to some glitch in NetSuite/Celigo the orders were created by real time flow did not have eTail IDs. Later the Scheduled order flow kicked in and created duplicate orders. This led to duplicate fulfillment and shipping of products. This was a revenue loss to the company.