If you do what I suggested, you will probably get a notice from the IRS saying that you didn't report the 1099-MISC. You will have to reply to the notice explaining that the 1099-MISC was issued improperly by your employer for income that should have been included in your W-2, and that the amount from the 1099-MISC is included in the wages on Form 4852. In the explanation that you have to enter for how you calculated the amounts on Form 4852, it might help to mention that you included wages that were incorrectly reported on a 1099-MISC, but mentioning it in the explanation will probably not be enough to head off the IRS notice.
