Hi Mike
Sounds like your system has been customized to work like that, out of the box the Job invoicing works as follows:
You open the "Job create sales invoice" batch from the search block or jobs menu
Specify the job number to invoice and set filters on what job tasks to invoice (The higher level in your example)
Under options you specify if the system should display the actual tasks or summaries the job
Clicking OK has the system create the invoice
It is possible that the create invoice batch may still be there and may still work, but not understanding the customization done to your system i cant say if it will work on not
I would suggest that you try searching for this batch on a test system then run it and test to see if it works, and you should also discuss it with your NAV partner as they may have some background on the customisation
Shout if you have any other questions
Cheers
Nev