If an amendment was filed by the company the IRS program should NOT spit out a letter. But if it does, you simply respond that the company incorrectly completed the 1099 erroneously and provide a copy of the revised 1099. An employer HAS to correct the 1099. It's the LAW. If they don't, you report the company to the IRS and let the IRS deal with them. And for the person who stated have the company prepay, they obviously don't have a clue regarding how the contracting world works.
