Any excess contributions for 2024 that have not yet been withdrawn, you can still withdraw before April 15, 2025. Please do so!
When you go through the HSA interview on your amended 2024 return, you will get a screen from TurboTax telling you how much was in excess. You have already ready withdrawn part of that, so now tell TurboTax that you will withdraw all of it (assuming that you have the cash in the HSA).
You have already contacted the HSA custodian to withdraw part of the excess; now contact them again to withdraw the rest.
This second 1099-SA won't show up for a while - perhaps not until early 2026 - after all, it is normal that the 1099-SA reporting on withdrawn excess contributions gets entered into the next year's return.
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