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You can manage & track your card collection and decks once you create an account and login.
The card under Hot Rod is basically out of play for a while. Its not considered on the battlefield, even though thats where it is physically, so none of its abilities apply. If its an Upgrade, that Upgrade isnt on Hot Rod, and so on. Its also not in your scrap pile, so it wont be shuffled into your deck when its empty. The card is used by its bot mode ability.