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I may be wrong about this, but I believe that if you simply change the affiliation of a minor league team to another team, all the players currently on that team move to the new affliated team. When I've done this in the past I've moved the players on the team (i.e. the double A team) to a different level so the roster for the team I'm changing affiliation for is empty. After the change is made I have the AI do a minor league set-up to redistribute the minor league players to the appropriate level.
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