The Flight Command upgrades apply for your whole fleet if you trigger them correct? Ie, if I discard a squad token, do all of the ships in my fleet benefit from the increased squadron speed if they activate squads?
Yes that's how they work but obviously on a turn when the Pelta spends its Squadron token you have to wait for each of your ships to activate to benefit.
I assume if the Pelta is destroyed before say your second ship can activate then that ship can no longer use the +1 speed to its fighter activations.

