That last quote "Filed pursuant to section 301.9100-2" is normally for amended returns, which you don't seem to need, because you did indicate that you would withdraw the excess on your filed return, and you initiated the request to do the withdrawal before April 15th.
Do you have any record that you initiated the request with the HSA custodian prior to April 15th? To my mind, that it all you need. You should not be held up because the HSA custodian is slow. A screen shot of the log on the HSA website or even an email from the HSA custodian would serve you well.
Whatever you have, put it in your tax files with your returns, just in case anyone ever asks.
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