Because there is no equivalent to Form 4852 to enter a substitute Form 1099-SA, I think it would be appropriate to enter a code-1 From 1099-SA and file with an explanation statement, but that can't be done by e-filing. Alternatively, you could enter the code-1 Form 1099-SA and e-file without explanation, then if the IRS questions your tax return you could provide explanation at that time.
