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@Grammy wrote:

So I have to file the Sch C on that EIN and disregard any payroll, (paid as a sub S employee) 

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Wait, you don't file a Schedule C if they are electing to be treated as a S-corporation (assuming they qualify for the late election).  Just paper-file the extension, and because you are making the qualifying late-election with the actual tax return, that should be able to be e-filed.