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If I have a Weapon in the upgraded character’s Armor slot and Tooth and Claw is removed from the character, what happens to the Weapon?

It stays where it is. Once an Upgrade is legally put into a slot, removing what made it legal to put it there doesn’t matter.
Source: Wizards of the Coast (2019-03-01)    【Link to Ruling】
Tags: Tooth and Claw