I'd have thought that if it is successfully recovered that there'd be enough of the original flight left that the carrier would only need to 'top-up' the flight and it's troops, meaning that it would retain it's original troop point.
As far as I can see, the rulebook has recovered flights relaunching in the same state they originally did (remember there was a ruling that EA fighters got there afterburners back if they landed or recovered in 1E ? Similar case I'd think.)
Destroyed flights that don't manage to recover (fighters or pods) may still get the odd one or two craft back home, which the carrier can then use to replace losses of recovered flights, as well as using the reserves on the ship (which might require only a fraction of a troop point anyway).
