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No, you will not add the contribution amount from your W2 again. However, you will go through the interview to answer other questions on your 1099-SA form. Again be sure to delete any duplicate contribution amounts that you may have entered.
Adding a 1099-SA (a distribution) can't by itself create an excess contribution situation. You would have an excess contribution situation if you double-counted your contributions, or if you did not indicate you had qualifying HDHP coverage. The 1099-SA would show up as taxable income, unless you check the box that says "I used all the money for qualified medical expenses," but it would not show up as a contribution.
This was it! I didn't realize I had a qualifying HDHP coverage. Thank you so much!
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