I’m interested in what @dmertz has to say about this latest question, but (just in case he/she isn’t available for a while...) I believe your filing now with the corrected number would be fine. The important thing in taxes is accuracy (even if there are otherwise some loose ends in the circumstances...), and your return’s HSA reporting would be accurate.
@Anonymous50, the worst-case-scenario is that it’s somehow processed before the new 1099, with the IRS system prompted to contact you about the discrepancy. But even that somewhat unlikely situation should be easily resolved with just a little communication...
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