I think if you have documented on paper everything that you did and why and saved it in your tax files, that you should go ahead and try to e-file. The IRS doesn't really want explanations on paper on a paper return, unless they specifically ask for it (they do sometimes, but not here).
Yes, changing the 1099-SA may trigger an audit, but it's unlikely in these days of a weakened IRS (the $80 billion has not yet made a real effect). And you are right that you did whatever you could to make your return correct and paid all taxes and penalties, so perhaps you would even join the small but not insignificant number of taxpayers who actually are issued refunds after an audit.
So document what has happened and why, and if you ever get a letter about this, you will be prepared.
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