You may amend your tax returns any time that you would like. A claim for a refund, however, must be filed within 3 years from the time the return was filed or 2 years from the time the tax was paid (whichever is later). if you amend your tax return and the amount of income reported does not match the amount reported on the 1099, then the IRS may deny the amendment to the return or otherwise conduct an audit. At a minimum you would want to fully disclose your position when amending the return and your basis for doing so.