If the swap occured without notice of the umpire and the #3 batter (Charles) scores while the #2 batter (Baker) is still on third, the the only reasonable conclusion would be that Charles passed Baker while running the bases. Call Charles out via 7.08(h). If still less than 3 outs, leave Baker where he's at. Leave Batter where he's at. Eject Charles and Coach when they start arguing with you.
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