Brandon, are you using the Online or desktop products? I ask because the HSA question occurs in the Online product (although I suspect it is in a different place than before). After you enter the numbers for the 1099-R, there is a screen that asks - "Do any of these situations apply to you?". In the middle, you can check "I moved some or all of this money to my HSA as a one-time contribution".
Once you check this box, continue, and you will be asked for further details (like how much of the distribution went into the HSA).
I am still looking at the desktop product.
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