Best way to send Pick/delivery note to DC so they can pick and confirm shipment via EDI.

Our company sends orders to the DC or Warehouse with the Delivery note. The delivery can be updated with Goods issue no problem if all items have no variances. We have issues when the quantity is 1 and DC has zero, the line is not updated to Zero quantity shipped and has an edi fail as Delivery cannot have zero or EDI transmission back is 1 line less than expected results of the Delivery Note.
The warehouse can make change from 2 to 1, as the delivery has 1 on the line and customer invoiced for 1 so all good. I am wondering if we used picking ticket to DC and once picked, it would come back into SAP and create the exact delivery note from the picking ticket and then I have no edi failures and warehouse picks will be invoiced if over and or less than expected. In Summary, sending a delivery that is not really changeable to the DC does not work effectively, and wondering if there is better process to work with Third Party WHMS system edi back into SAP for confirmation of goods shipped and Posted and invoiced.
Your comments appreciated, John Pearson