I believe the answer to this question is two-fold and sort of confounding.
The answer is "Yes, you can e-file an amended 1120-S return with TurboTax Business" but also
"No, you cannot e-file using the same file with which you originally e-filed".
In other words, you can start a new 1120-S as an amended return and e-file that return (since that file has never before been e-filed). Alternatively, you can transfer the prior year's 1120-S into the program, mark that return as amended, and e-file that return.
The problem is, basically, even though you have saved the original e-filed return under a different filename, you are still using that same file to amend the return (and that is the return you already filed, which is what TurboTax is flagging).
