I did a search and my HSA does not have a contribution correction form, only a distribution correction form and return of excess contribution form. The difference between return of excess and contribution correction seems to be the 1099-SA. In other words, the return of excess generates an (incorrect) 1099-SA and a contribution correction does not generate a 1099-SA. So it would seem (agreeing with you) that option 3, deleting the 1099-SA from turbotax would be consistent with "as if it had never been done". But as we say, it increases the audit risk. Maybe a statement included with the tax return would help. This is complex, but it is beginning to make sense how to handle it.
