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They should, unless the diagnostics instruct you otherwise. FWIW, see this thread for Intuit's response to this exact question but related to ProSeries: https://proconnect.intuit.com/community/proseries-tax-discussions/discussion/e-filing-an-amendment/0...
Think of the thousands of amended returns IRS has already been preparing for years. Those are the ones that result in a CP-2000 notice. An IRS examiner looks at a screen that shows data from the original return. It is not in the format of a paper return, even if that is what was filed. Another screen shows the income that should have been reported. If it is not on the return, the Automated Underreporter program adds it in, recalculates the tax and selects standard paragraphs to explain the change.
The major difference between processing a CP-2000 case, and an amended return, is that the data changes come from the taxpayer and not from information returns like 1099's and W-2s. Ask yourself, “What data from this return does IRS already have in its system?” Then, don’t send it to them again. What you see on your computer screen, is usually not what they are going to see on theirs.