If you change any numbers on a form like the 1099-SA which the IRS has a copy of, this is more likely to draw the attention of the IRS that doing what we talked about above. Once reason that the IRS gets copies of forms (like your W-2 and 1099s) is to compare what you reported with what they hears from other sources.
Since your HSA custodian won't co-operate in correcting their mistakes, there is no way that you can file a clean amended return.
Just document EVERYTHING in case the IRS ever asks.
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