It should be possible to process one invoice for transportation services that includes more than 1 freight bill. Transport vendors send invoices that include more than 1 contracted service, this can be daily or monthly. They don’t send one invoice per freight bill.
Now in D365fO you can only generate one invoice per freight bill and you cannot use the same invoice number for another one.
There is a workaround about adding lines to the previously created freight invoice with the details of your other freight bills. However the lines need to be filled out manually. So they can just go back to the Freight invoice details form, click New on the line and enter the information there.
The process should be easier and more automatic.