The tax procedures that exist for this situation only apply if the repayment occurred in a different (future) year from the payment of the bonus. If the bonus and repayment occurred in the same year, the employer is supposed to net it out on your W-2. They can't correct box 2, since that was what was originally sent to the IRS in your name. But they should change box 1, and when you report lower wages, you would get a refund of the excess tax withheld.
The same answer applies to state income tax.
If they adjusted box 3-6, they should directly pay you (refund to you) the adjusted amount of medicare and social security taxes.
Contact them and explain that since the wages were repaid in the same year, they are supposed to net it out in box 1. If they refuse, you can use what's called a substitute W-2 form to report the adjusted amount. But this may delay your refund and the IRS may ask for proof, so make sure you keep all your records including the bonus, repayment, and all your correspondence with the employer.
