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What happens if an opponent’s card tries to scrap a Weapon and an Armor from the upgraded character at the same time? Can Spare Parts save both of them?

No, Spare Parts can save only one other Upgrade. You choose whether it saves the Weapon or the Armor. Spare Parts and the other Upgrade will be scrapped.
Source: Wizards of the Coast (2019-03-01)    【Link to Ruling】
Tags: Spare Parts