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Yes, you need to send the amended tax return, Form 1040X and Form 8889. Form 8889 will provide the information that the distribution was for medical expense and hence will not be taxable on Form 1040X.
Let me know if you have any question.
Please note: This advice is provided with the understanding that all the relevant facts have been provided by you. Any change in facts might affect the advice given and hence may not be relied on in such cases. Nothing contained in this reply was intended or written to be used, can be used by any taxpayer, or may be relied upon or used by any taxpayer for the purposes of avoiding penalties that may be imposed on the taxpayer under the Internal Revenue Code of 1986, as amended.
Are you filing the amended tax return with a tax software?
If yes, than the software will automatically create the form when you fill in Form 1099 SA info.