"the amount refunded back directly to the HSAs by the hospital is NOT going to be reported as a contribution for 2022."
Well, this is good.
"if I understand correctly, I should report on my 2021 tax return the full $6000 distribution since that is what is on my 1099-SA. "
Yes, it's always preferable to have your numbers correspond with the numbers on forms that the IRS gets copies of. Besides, if I got your story right, you did indeed spend the whole $6,000 on qualified medical expenses.
"Then in 2022 I received the refund of $3900, which was recorded by HSA Bank as a "gross distribution" of negative $3900. So if for example I spend $5000 this year on qualified medical expenses (which I will), then on my 1099-SA for 2022, it will show $5000 - $3900 = $1100; is that how it works?"
At this point, I don't know what they're doing - this is beyond what the IRS describes in Pub 969 or what the IRS has published in a variety of notices. In fact, for Box 1 on the 1099-SA, the IRS says explicitly for the HSA custodian: "Do not report a negative amount in box 1" which they would have to do if you spent less than $3,900 in the current year. I don't see where they're going with this, but never mind, because you are going to complete your tax return as accurately as you can, and if there's ever an audit, you will show them all the paperwork to explain why you did what you did.
"The 5498-SA for both 2021 and 2022 should match what is on my W2"
I wouldn't worry too much about matching numbers between the 5498-SA and the W-2s. For example, Box on the 5498-SA contains
(1) Enter the total HSA or Archer MSA contributions made in 2021,
(2) Include any contribution made in 2021 for 2020 (!),
(3) Also include qualified HSA funding distributions (trustee-to-trustee transfers from an IRA to an HSA under section 408(d) 9)) received by you during 2021, but
(4) Any excess employer contributions (and the earnings on them) withdrawn by the employer pursuant to Notice 2008-59, Q/A 24, available at IRS.gov/irb/ 2008-29_IRB#NOT-2008-59, should not be reported as a contribution.
So you can't quickly compare numbers from here to there; instead, you have to sit down with a spreadsheet, and see the totality of what has happened.
Really, the most important thing is the HSA custodian not report the refund as a contribution for 2022 - everything else is reasonably trivial. We were worried because we know that other HSA custodians have reported such refunds as contributions.
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