Technically, the IRS does accept e-filing of superseding returns.  Some tax software programs do allow that but not PTO or Lacerte.

If you are not filing that as an amended return, you will need to file the superseding return on paper but make sure you do the following so that "Superseding Return" will be shown on top of the 1120.

1. Click on General > Miscellaneous Information;
2. Click on the Miscellaneous tab;
3. Scroll down to the line Explanation on top of main form [Override] and enter "Superseding Return" without quotation marks.