After you file

The most reliable way to do this is to let the program delete the 1040X form for you:

1. Make a copy of the .tax20XX file that you used for your 1st amendment.
2. Rename it so it is obvious this copy of the file is for your 2nd amendment.
3. Open TurboTax by double-clicking on the application logo and NOT by double-clicking on the Tax file.
4. On the title screen select "I need to file an amendment".  It will ask you to open a tax file.
5. Open your 2nd amendment tax file.  It will ask you if the IRS accepted your 1st amendment.  Say Yes.
6. When you proceed it will tell you it needs to remove the 1040X from your 1st amendment.  Do it.
7. Follow the procedure for making an amendment.

Thanks to user jeking3 for this solution

https://ttlc.intuit.com/community/after-you-file/discussion/how-do-i-do-a-second-amendment-gt/00/451...