This has been a confusion as long as FLEX has existed and we have discussed it several times without a real resolution.
In the OP, by the time the DP bats, there have been three violations. If the #1 batter batted after the FLEX, then the FLEX either
- illegally batted or
- BOO for the DP, which means the #1 also BOO.
The OP implies the appeal was after the DP batted before anything else occurred. The DP was not replaced by the FLEX if she batted and is not BOO at that point because she followed #2 batter.
So, the penalty has to be for the FLEX batting at all, as above depending on rule set.
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Officiating takes more than OJT.
It's not our jobs to invent rulings to fit our personal idea of what should and should not be.
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