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To make any change, file a new form W-4 with your employer. This will change the amount that comes out of his paycheck.If his employer insists that all W4 information be made online then he would log back on to the employer's online system and make the change to 0 for his allowances.
If they do not care he can complete a W4 form and turn it into the Human Resources.https://www.irs.gov/pub/irs-pdf/fw4.pdf
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Did your son correct his error yet?