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You can manage & track your card collection and decks once you create an account and login.
The cards under Wingspan are basically out of play and are used to count the bonus for Wingspan's alt mode ability. They're not considered on the battlefield, even if that's where they are physically, so none of their abilities apply. Those Upgrades aren't on Wingspan, and so on. They're also not in your scrap pile, so they won't be shuffled into your deck when it's empty.
