I have no idea what answer you are referring to, but to repeat:
1. If you have an amount with a code of W in box 12 on your W-2, you should enter this when you enter your W-2.
2. In the HSA interview, when you see "Let's enter [name]'s HSA contributions", there are two lines. The first line has the code W amount from your W-2 and it cannot be changed here. The second line is for you to enter any "direct" or "personal" contributions, that is, any contributions that were made to your HSA that were NOT through your employer.
No part of the code W amount from your W-2 should be placed on that second line, or else, as you noted, you will get a double deduction and a likely excess contribution error message. This commonly happens when taxpayers know that part or all of the code W amount is their contribution by means of payroll deduction and so despite the explicit warnings not to put any part of the first line into the second line, they do it anyway.
@cesium62
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