Yes. Either the pitcher or the batter may be substituted for at any point in the at-bat. Only if it is not the first hitter that pitcher is facing, if it is the first batter he faces, he must pitch the entire at-bat unless injured, then he may be removed from the game
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Yes, during the windup, so long as it's his normal pitching style. There are many pitchers who tap the inside of their glove with the ball prior to winding up for the pitch. It must be done in such a way as to not cause deception to the batter or umpire.
Before the windup and with runners on base, the pitcher cannot do so. When he is standing in the Set position, he must hold the ball with both hands and come to a complete stop before going into the windup. At this time, he may not take the ball out of the glove.