I am not sure that the IRS anticipated such a contribution when HSAs were placed into action in 2004, but we can approximate what to do.
In the 1099-R interview, don't enter anything about an HSA in this dialogue (but since it's a pension instead of an IRA, it probably won't ask).
In the HSA interview, proceed through the input screens until you see "Did [name] put money into an HSA in 2021?"
Skip the next screen that says "Let's enter [name]'s HSA contributions".
On the next screen where it asks "Did your employer tell you about any other contributions?", answer YES, and three new lines will appear.
On the last line ("Employer and payroll contributions not reported in Box 12 of your W-2"), enter the amount from the 1099-R.
This will cause the pre-tax HSA contribution to be handled correctly, even if it looks odd.
Write a note to yourself on why you did this and stick it in your tax files.
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