Best Practice for Exchanging or Adding Items to an Order

We are in the process of developing a seperate Warehouse Managment System for use with Netsuite.   I had a question regarding the Best Practices for adding or exchanging items during fulfillment.  For instance, if for some reason , Netsuite is over reporting quantities and I need to exchange the item, or a sales rep in the field calls in a request to add items to an order before shipment the current process is that we need to go back to the sales order to make the changes and then fulfill the order.  Unfortunately, to do some like this in the WMS would be complicated since you will need to either adjust the order in the WMS and then have it update the order in Netsuite and then be able to create the fulfillment.  Is this the only