When you went through the steps, finally deleted the 8889-T and 8889-S as instructed, did you look to see if the 8889-T and 8889-S actually went away?
For example, if you have the code W in box 12 on your W-2, and you don't delete the W-2, then when the 8889-T is deleted, it won't actually go away - it will come right back to the list. This means that the data for your HSA doesn't go away, including the excess employer contributions withdrawn.
I have never seen this not work (except for the IRS to HSA funding distribution).
Here's a thought - when you delete the W-2, the 1099-SA(s), and the 8889-T and -S, if there is a 5329-T or a 5329-S, would you delete that as well, and come back and tell me what happened? Thanks!
@zauschhaus
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