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Get your taxes done using TurboTax
Paying for Premier does not mean the import process works perfectly when you import W-2 data. Anyone can import a W-2 even using the Free Edition. Sometimes the data that is transmitted during the import process is inaccurate--the error can come from the employer end. The user still needs to check its accuracy before filing. It is important to obtain a hard copy of your W-2 each year. Going forward, do not count on just importing a W-2 and not getting your own hard copy from the employer. You are supposed to save your own copy of a W-2 for at least three years. If you get your own copy you can check it when you import the data.
If the IRS says not to amend, why would you think you should amend? It sounds like the IRS corrected the problem and adjusted your refund. TurboTax does not receive any information from the IRS after you file, so we cannot see the letter the IRS sent to you. You should follow the instructions given to you by the IRS.