My memory suggests that the original format of the Shuttle call sign was along the lines shuttle 1 Alpha where 1 indicated the route and direction (so, for the sake of argument 1 = LHR/GLA and 2=GLA/LHR, 3=LHR/EDI etc). The letter indicated the sequence so 1A was the first LHR/GLA 1B was the second LHR/GLA. By doing that they overcame any issues relating to flight numbers because they never really knew when they might have to insert a flight into the schedule.
I once asked a BA shuttle manager if he took any notice of reservations (because connecting passengers, in particular, could be booked). Well, he said, I did once ask just before Christmas how many reservations we had for Belfast and when they told me I borrowed a Tristar but I didn't really need it.