Did you use TurboTax Business? You could not have used online TurboTax for returns for a C corp or S corp. Your issue does not sound like a do-it-yourself project at all. You should seek paid professional tax help.
The statute of limitations has run out for 2015 and prior years for filed returns.
If you filed timely S-Corp returns and 1040s for 2015 and prior, you can't amend them.
The statute of limitations does not run on non-filed returns.
Please see this IRS website: Statute of Limitations
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