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I'm claiming a tax credit based on IRC 1341 this year because I repaid my income of 4600 back to my employer in 2011 for an overpayment made in 2010. Will this increase my risk for being audited?
No, I have prepared maybe half a dozen Section 1341 (Claim of Right) claims. Never heard "Boo!" from the IRS. The most I can imagine would be correspondence asking you to document the repayment.