We've also discussed what a flagship is, and why it wouldn't necessarily convene a bonus to your fleet. A flagship can mean the main ship in a fleet, or it can be the first thing (ship, product, service, person, whatever) of a given catagory. ie If sins was the first game the IC made (and I almost think i heard it said that it is) it would be the flagship game for IC.
Hence, when you loose your flagship, you loose the first cap ship you made, and hence you couldn't re-designate another as your "first" because "first" is final. If that made sense.