You can file an amended 1120-S if you did NOT file an original 1120-S with Turbotax Business.
I fully comprehend that it doesn't make sense to you, but that's how the program functions with respect to checking the EIN, e-mail address, registration, etc., against the original return and the amended return.
I have actually done test returns in past years and a test amended 1120-S that I e-filed did not get transmitted after I e-filed a test original 1120-S (similar results obtained with a test 1065).
