Go ahead and enter the 1099-R (I assume that you received a 1099-R with a distribution code of 7 and that the source was a traditional IRA). Answer that you did "something else with it", and finish the rest of the 1099-R interview. The income will show as taxable, but don't worry, taking the steps below will correct that.
Now go to the HSA interview (if you need to, do a Search on hsa and click on the Jump to hsa link (Mac users must find HSA in the Topics List). Put a checkmark next to HSA, then navigate through the interview until you see a screen titled "Let's enter [name]'s HSA contributions". On the second line where it says, "Any contributions you personally made", enter the amount of the IRA distribution here.
This will cause the HSA contribution to appear on line 2 of Form 8889. Now, this won't appear on line 10, but you will see that line 12 will be the same in either case, so your return will be monetarily correct.
The net result is that the 1099-R will be added to income on line 4b on Form 1040, and that same amount will be subtracted back out from income on line 12 on Schedule 1.
One last thing, put a note in your tax file explaining what you did as a workaround in the unlikely event you receive an inquiry. @TK32 I have edited my original response in which I did not take into account that you were reporting HSA contributions from a 1099-R distribution. [Edited 02/19/2021 2:50 PM PST]
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