Thank you to everyone that replied to my message I really appreciate it. However my colleagues and I managed to get a workaround to it and this is how to do it.
1. First of all you need to find the shipment numbers for the original order lines and note these down
2. Then select the charge line on the original order and click Line - Related information - Item Charge Assignment
3. This opens the following screen where you can select Get Shipment Lines
4. Select the correct shipment from the list provided by clicking on it and fill in the Qty to assign in the next screen. You can check that the remaining to assign is showing as zero and close out of the screen.
5. You'll be then able to post the order and create a final invoice for the missing charge items.
