Army used to do a similar thing over here in Europe, but have since stopped. I think it was just an aid to help our Theater Flight Operations office keep track of which leg the flight was on. For example, a flight in one day from Stuttgart to Naples would be Clue32A then on to Venice as Clue32B and back to Stuttgart as Clue32C.

This confused the occasional pilot and made the Serbians mad as they would approve, say, a JGO48 to overfly their country but a JGO48A would show up. Diverting from overhead Bosnia when you are 45 minutes from landing in Kosovo out over the Adriatic to avoid an entire country sure puts a damper on your day.