Navision allows you to post multiple shipments and then combine all the shipments into one invoice. To do this:
1) Go to Sales & Marketing --> Order Processing --> Invoices
2) Create a new Invoice
3) Click on Function --> Get Shipment Lines
4) Select all the lines that you want to combine and then click on the OK button. Navision will copy all the sales shipment lines to the Invoice Line.
5) Click Posting --> Post.
6) Click on the Yes button to confirm on the posting.
Sales Order posted with this method will not be deleted from Navision even after fully invoiced.