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When Private Pteraxadon is in weapon mode (AKA Binary Edgewing Scythe), it says the defender's base armor value becomes zero during this battle. Does that count any armor bonuses from upgrades as well? Or does it only apply to the printed value on the bot?

Private Pteraxadon's weapon mode ability specifies that it only applies to an opponent's base defense, so it would not include defense from any upgrades or flipped battle cards.
Source: Wizards of the Coast (2019-07-12)    【Link to Ruling】
Tags: Private Pteraxadon, Air Command • Artillery