Users can not modify the QlikView document through the server beyond the creation of bookmarks, notes and Server Objects.
When it comes to develope over a QlikView document they need to use the QlikView Desktop (which I believe they are already using base on the error that you say they get).
The licensing of the QlikView Desktop has nothing to do with the fact thay they have Named CALS or Document CALS assigned.
If you want to license their QlikView Desktops, they can use the "Open in Server..." and by opening one single QlikView document, QlikView Server will lease one Named CAL to license that specific QlikView Desktop allowing that user to modify or create as many QlikView documents as they want for 30 days (after 30 days they have to renew their license).
All this is possible as long as your server is not a Test Server and the check: "Allow license lease" is activated on the Management Console => System => Licenses => Server => CALs