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When KO’d, a Battle Master comes back as a weapon. Then once it gets destroyed, it goes into the KO area. My question is, can you flip it back to bot mode in the KO area after it falls off?

No. You may only flip characters in the KO area using your normal once-per-turn flip.
Source: Wizards of the Coast (2019-05-02)    【Link to Ruling】
Tags: KO