3 minutes ago, Parravon said:But you shouldn't bring a bias from another system into this, because it's not relevant. The Damage Deck and the Discard Pile are two very separate things, so you cannot go searching the Discard Pile for a card. The rule for replacing the Damage Deck only comes into play once the Damage Deck is used. It doesn't apply only when specific cards are used. It must be the deck in its entirety.
They should be going to the Discard Pile when a ship is destroyed, not stay on the ship card
When it is destroyed, they do. But at the time you assign them the ship is still in play. Only when the attack is concluded and the damage is dealt does the ship get destroyed. So technically you do put them on the ship's card no matter what.