1st - if there is any upgrade or downgrade of shipment method. DGN will need to update this in RMA document (which u have done so) and also need to update the shipment method in the system. By updating the shipment method in the system, when u do a "re-create" in the system, it will show the correct chargecode. This is the standard way of amending in the system if there is any upgrade/downgrade of shipment method.
But you need to make sure that this is all checked before you send the final draft to JNE billing team to check..