So you will need to adjust your Wages to add that $4,000 to them. This so that your Wages are equal to your salary less $4,000 (which is what we were hoping your employer would do).
To adjust your Wages, go to Personal Income (or Income)->Less Common Income->Miscellaneous Income, 1099-A, 1099-C and click on Start or Revisit. Note that the exact navigation varies somewhat from product to product.
On the next screen, go to the bottom and click on "Other Reportable Income".
So Yes to "Did you receive any other reportable income?"
For Description, enter something like "Wage adjustment for W-2 issue with code W in box 12" - It needs not be completely clear; it only needs to remind you what it is talking about on the return.
Then add the $4,000 (positive this time) to the box next to your name. This will increase your income to compensate.
Good catch!
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