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I think that's because once they become affiliated, reputation no longer matters. Reputation is used to see if players want to sign as free agents with certain leagues (MLB and Japan have more cache with players than European leagues, for instance).
Players don't directly sign with AAA and AA clubs. They sign with a major league club and are then assigned to minor league clubs as part of a development system. (There is some level of "reputation" there in that an established major league player may refuse to play in the minors altogether.)
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