The reason TurboTax removed the Refund Meter from its prominent place on the screen was because some things go on in the background that aren't immediately clear on a screen to screen basis. This confused taxpayers who expected everything to be done when you changed screens. For example, what could be happening to you is that the amount on the 1099-SA is being added to income immediately when you enter it. Then, a screen or two later you make an entry and the HSA distribution is removed from income, which is proper.
Do me a favor, if you would: don't watch the Refund Meter too closely. At the end of the HSA interview when you see the HSA summary, then go look at your 1040 and see if the 1099-SA has been removed. It should not appear (I think this type of "income" would appear on line 8f on Schedule 1 of the 1040), but as I said, it should not be there if you completed the entry for the 1099-SA correctly.
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