I assumed you were trying to exclude income based on a tax treaty with a foreign country. If so, you first need to report all of your income, including the income that you are trying to exclude, then you enter a negative adjustment to remove the income exempt by treaty.
You mention income reported on a W-2 form and on a form 1042. You also mention a treaty. You also said that income is not allocated property between the W-2 and form 1042. Are you simply trying to change the reporting of income between the W-2 and Form 1042? If so, and if the W-2 income should be lower than reported, it would lower your social security and Medicare tax if that is listed on the W-2 in boxes 4 and 6. If that is the issue, there is no way to recover excess social security tax on your personal tax return form 1040 in this instance, you would have to get your employer to amend the W-2 form for that. If you are simply transferring the reporting of income between your W-2 and form 1042 entry, then it would not likely affect your income tax, as the total income would be the same either way.
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