As a practical matter, the S corporation return is not critical with respect to state tax filings. It is just an information return that shows no tax liability in most instances. Your personal federal tax return, to which the S corporation return flows, is used by the state to aid in the verification of your state personal tax return, not so much the S corporation tax return.
So, you can go to a preparer and have the amended return prepared and e-filed, which will entail preparing the original return again, or you can document that you filed the amended return with the state and they refused to accept it, and let it go at that.
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