I told my HSA custodian that this (above) is how I plan to proceed, @dmertz. However, their response to me this afternoon suggests they have a totally different plan for addressing this. Here is what they said they're planning to do:
For 2021, they would complete a form 1099-SA with distribution code "2" and $475.01 reported as sent back as a distribution.
For 2022, they would amend the 2022 5498-SA. They would process the correction as an "Excess Contribution Reversal" which will remove it from reporting on the 5498-SA, in their words. This is where they must've been confused as to why I would request less than $3,600 to be removed, as they are planning to amend the 5498-SA rather than leave it alone and file a 1099-SA.
For 2023, they would remove the full year's contribution of $1,800 as an "Excess Contribution Reversal" as well, and remove it from being reported entirely. The gains of ~$126 would be sent back and reported on the 2023 1099-SA in box 2.
Does this sound right to you? Or do I need to request they file things differently? This is a fairly reputable HSA custodian, so if this is incorrect, that means that they're processing many of these incorrectly for people. @Opus 17, do you want to weigh in on this as well?
