"If IRS asks in future about the discrepancy between 1099-SA that they have from my old HSA trustee and what I mentioned in the tax return, I could tell them the same and probably show the medical expenses if they ask for it."
Yes, if the IRS asks, explain that you did a Mistaken Distribution in the form of the withdrawal of excess contributions which were, in fact, not in excess. And because you subsequently closed the HSA, you were unable to fix the situation the right way, so you changed the distribution code in order to report the 1099-SA (better to report it wrong than to ignore it all together).
Then, if the IRS wants to talk to your HSA custodian about fixing this a more elegant way, they will have that opportunity. Otherwise, you have documented everything and are not holding anything back.
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