The rule is 3-1-1 not 3-3-1. It's also not relevant as the shortstop is not a substitute under 2-36-1 as he is not eligible to replace another player in the lineup as he's already in the lineup. The relevant rule instead is 2-28-1:
"The pitcher is the player who is designated in the lineup as being responsible for delivering (pitching) the ball to the batter."
Ironically, there doesn't seem to be a proscribed method for changing the designation.
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