The IRS generally allows you to file an amended return (Form 1040-X) to claim a REFUND within 3 years from the original filing date or 2 years from when the tax was paid, whichever is later, but if you need to correct the income you should file an amended return.
However, since the state said they made the adjustment due to the change in the federal income, the IRS may have already made the adjustment. You should review the notice that the state sent you carefully, and if you do not agree with the assessment you can prepare the amended returns and submit them to the state with the corrected amounts. (Note because you did not report the income correctly, interest was most likely added to the amount you owed.)
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