Yes, you are faking out TurboTax...but you couldn't e-file the "original" return anyway because it was already done through your CPA (I presume it was e-filed).
However, you will have to print and mail the amended return - TurboTax does not support e-filing amended returns (it may next year).
The IRS does not care who is doing the original return and the amended return. All they know is what you (or anyone) sends to them.
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