Thomas answered your question in the first post:
You should use the corrected W-2 numbers on your tax return. The excess taxes will be returned to your employer when the corrected payroll forms are submitted by your employer. So, the IRS will find out about the excess when your employer submits the corrected W-2 form and associated payroll tax returns. Then, your employer will have to reimburse you for the excess taxes you paid in.
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