"he cannot do that because it already passed their deadline of fixing errors for 2024" - Actually I am happy to hear that, because too many HSA custodians really have no idea how to apply the HSA regulations. However, this leaves more work for you.
First, you will need to determine at what point over the year, your contributions became excess. You start your earnings calculation from that date with the amount that is excess.
Then to calculate the earnings, please look at the following paragraph from page 3 of the Instructions for form 1099-SA:
For HSAs and Archer MSAs, if you are reporting earnings on a distribution of excess contributions, use the method under Regulations section 1.408-11 for calculating the net income attributable to IRA contributions that are distributed as a returned contribution. If the amount in box 2 includes earnings on excess contributions, enter distribution code 2 in box 3.
Unfortunately, I can't do the calculation for you, because that would have me crossing the line into being considered to have substantially done your tax return (i.e. I would have to sign your return).
At this point, you might seriously consider having professional help to do your return. As you surely have noticed, TurboTax would happily do your return for you (meaning everything, not just this section 1.408-11 calculation). Please see TurboTax Full service.
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