You received a 1099-R from the IRA custodian, right? In the screens after you enter the 1099-R itself, there should be a question that asks what you did with the money, and when you say, "I did something else", it should ask you if you put any of it into your HSA.
It is possible that you have to show that you have an HSA before this screen in order to trigger this. If there is a code W in box 12 of your W-2, then TurboTax will know from that point that you have an HSA.
Otherwise, you may need to do a Search (upper right) for hsa and click on the jump-to link, then indicate that you have an HSA, then go straight back to the 1099-R interview and go through it again. Then you can finish the HSA interview after TurboTax knows that you had the Qualified Funding Distribution your HSA.
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