If inventory is showing up as Shipped and Not invoiced, then the original transaction has only been shipped. You will need to go back to the original return order, update the $ amounts on the inventory shipped (to reflect your Vendors credit amounts) and then post the credit memo.
Essentially, you have only completed half of the transaction, the shipping. The Crediting/Invoicing still needs to occur on the original return order. I don't have any documentation that I can send you, because MS controls this material. But if you check with your Navision provider, they should be able to provide standard NAV documents. Ask them for the NAV 5.0 Trade manual.