Not sure that I would have called a time out to clean the plate without first calling the batter out for abandonment.
However the OP, time was called, therefore,
Under Rule 5-2-2-b, a runner may not advance when the ball becomes dead.
Once I noticed the batter still at home plate I would bring the ball live when the pitcher has the ball within the 16 foot circle and I (the umpire) calls and/or signals "Play Ball" and gives a beckoning hand signal (Rule 5-1-4)
Once the ball is live I will call the batter out.
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