yep they use it for everything and is the defacto flightnumber. Its all offical through the agency that deals with callsigns.
Some time ago, my FTO (headed by a Lufthansa captain) decided they want to be an airline and got their own airline flight IDs from whoever issues them. Now instead of using the aircraft's registration (which every student and instructor knows by heart), you have to use the right flight ID from a list. Often, people forget about this and then have to change the flight ID to the aircraft's registration in flight and vice versa.
Most stupid idea ever.