A corrected Form 1099-SA with all dollar amounts being zero properly indicates that the correction was to show that no distribution actually occurred, in this case because the HSA custodian accepted a "return of mistaken distribution" of the entire amount previously distributed.
After you correct the original Form 1099-R entry in TurboTax, if TurboTax sees the amount distributed from HSAs is zero TurboTax will leave Form 8889 Part II blank. However, to correct the previously filed Form 8889 Part II that showed a nonzero distribution the IRS needs to see an explicit indication on Form 8889 Part II that the amount distributed was $0. You'll need to manually create the corrected Form 8889 by replacing all of the nonzero amounts in Part II with $0 and provide that form to the IRS. If your amendment did not include a Form 8889 corrected in this way, your originally filed Form 8889 is still in effect and disagrees with the reporting of $0 distributed.
