After you file

tagteam is correct.,  Before amending the return, create a copy so that your original return remains intact. If you haven't done this, I suggest you remove the changes you've made on the 1120S and follow these steps:

1. Create a copy of the return.  While in the original return, click File > Save As.  Add the word Amended after the file name.
2. Go through and make the changes.
3. A 1120S will be created with the Amended return box marked.
4. You should now be able to e-file the return.