Rate and Qty change after delivery of a SO

I have following business scenario for my client:

The end user inputs a sales order with price and qty for several items . After pick slip, confirmation shipment and delivery note print my end user  creates proof invoice/pro forma invoice to share with customer( with Prevent Next Status Update=1 processing option) . At this stage customer again do some negotiation on price/qty. For example original rate is reduced , some received qty is returned etc. Accordingly my end user has to generate final invoice with updated qty , rate and price which definitely differs from original sales order. Please guide how can I do this qty and price update after creating the proof invoice. Since its in proof mode so AR entry will be not generated. After updating the qty,rate user will then generate the final negotiated invoice. Please guide. Thanks