You'll need to paper file a superseded return. TurboTax will automatically check the 'amended' return box for a return with any changes made to it. In this case you would print out the new return and make sure the 'amended return' box is not checked or you'll need to white it out or something if it is and then write "Superseded Return" across the top of page 1 of the 1120-S and make certain it is postmarked prior to the return deadline.
@Scodoboz