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To add onto what Prof A said, when I brought this up at Nats to have it ruled, it was also decided that in a case where a duplicate would be created by this scenario (band to their AuTO, exchange for your Samuel, opponent already has Samuel in his territory), the duplicate (yours) would be discarded by game rule after battle. Since there is nothing to restrict the exchange when it happens, but it has to be returned after battle by game rule, it creates one of those now-rare cases when duplicates can exist. The one originally there (their own Samuel already sitting in territory) stays, and yours would be discarded.
Are you the person who approached me about that? Man, I wish I would have connected your face to your board name at the time.