If a crit is received that prevents you from using a secondary weapon until the crit is resolved has energy on it, does the energy get removed or does it stay on the secondary weapon?

I am afraid I do not have my Epic Ship critical decks nearby, nor can I find the list of crits online.

Best I can say is that you should remember that Epic Ships have their own critical decks, and should not be assigned the normal cards, so Munitions Failure does not enter into it.

as far as I know It doesn't say anywhere to remove the energy, just that you can't use the weapon as long as the damage card on it is face up, I'm guessing you can either use the energy on it to flip the damage card, or save it and use energy from the main ship card to flip the damage card so you can immediatly use the secondary weapon

We played that you lose the energy. I dont have any official ruling, but it does seem more thematically appropriate, though, I guess you could argue some other piece of equipment has failed on the weapon and it's battery is just fine.