I believe that in the first situation you have an illegal player, who, since she was a courtesy runner in the same inning, doesn't have a legal right to that position. If discovered and protessted after one pitch or one play, the penalty is disqualification of the offending player and she is replaced by a substitute player or the starter.
The second situation is an unreported substitute who is disqualified, all outs stand, and all players are returned to their original bases.
As you can see, the penalty inforcement is different.
Now that's what I believe, but I can be wrong.
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