Are you starting the amendment process with the return as filed as the base ?   If not you must return the tax file back to how you filed it BEFORE you start the amendment process.  So delete the 1040X and put the return back to "as filed" condition then only start the amendment process.

How do I cancel or undo an amended return in the TurboTax CD/Download software?

If you started amending your federal return by accident and would like to cancel the amendment, follow this process to correctly "unamend" your federal return:

1. Open your return.
2. Switch to Forms Mode (Windows instructions | Mac instructions).
3. In the left pane, select Form 1040X.
   • Windows: After the form is generated in the right pane, click the Delete Form button at the bottom of the window.
   • Mac: From the Forms menu, select Remove Form 1040X.
4. Follow the on-screen instructions to remove the 1040X from your return

1. Important: Go back through the TurboTax interview and undo any changes you made after you selected the option to amend your  return, as merely deleting the 1040X will not undo those manual entries for you.

State Amendments

The best way to "unamend" your state return is to go through your state return from the beginning and keep your eyes peeled for amend-related screens or questions.

The amend question usually appears right at the beginning or towards the end of the state interview (never in the middle).

Correct any entries that have to do with an amended return, e.g.:

• Answer No when asked if you want to amend;
• Clear any amend-related checkboxes;
• Delete entries in the tax year field.
• Note: In a few state programs, you actually have to answer Yes to the amend question so you can revisit the screens that contain the information you want to delete.

If you still can't get rid of your state amendment form, try clearing your state return and starting over.

Use the FORMS mode to confirm you have the return back to the "as filed" state ...

This is my mini version of  a tutorial  that should be in the downloaded program: 

What is Forms Mode?

Forms Mode lets you view and make changes to your tax forms "behind the scenes."

If you're adventurous, you can even prepare your return in Forms Mode, but we don't recommend it. You may miss obscure credits and deductions you qualify for, and you may forget to report things that will come back and haunt you later.

Forms Mode is exclusively available in the TurboTax CD/Download software. It is not available in TurboTax Online.

Related Information:

• Why would I use Forms Mode?
• How do I switch to Forms Mode in the TurboTax for Windows software?
• How do I switch to Forms Mode in the TurboTax for Mac software?
• What is-the-meaning-of-all-the-different-colors-in-forms-mode

If you want to play around with different figures and tax scenarios without affecting your original return you can ….

• >>>In the TurboTax CD/Download software by creating a test copy: 
• 1.  Open your return in TurboTax. 
• 2.  From the File menu, choose Save As. 
• 3.  Give the copy a new name to distinguish it from the original (for example, by adding "Test" or "Example" to the file name). 
• 4. Click  Save. You are now safely working in the test copy and anything you do here will not affect the original. 
•  https://ttlc.intuit.com/questions/1900642-how-to-make-a-test-copy-of-your-return

• >>  use the WHAT IF tool: 
• - Click Forms Icon (upper right of screen) or Ctrl 2 (forms view) 
• - Click on the Open Form Icon 
• - In the “Type a form name.” area type What-If (with the dash), click on the name of the worksheet - click on Open Form 
• - You will see the worksheet on the right side of the screen; enter the information right into the form 
• - To get back to interview mode - click on the Step-by-Step Icon (upper right of screen) or Ctrl 1

Once you have filed successfully … you can shut off the auto updater function and then save the return &  .taxfile.

It's always a good idea to make a backup copy of your tax data file, in case your original gets lost or corrupted. Here's how:

1. From the File menu in the upper-left corner of TurboTax, choose Save As (Windows) or Save (Mac).
2. Browse to where you want to save your backup.
   • Tip: If you're saving to a portable device, save it to your computer first to prevent data corruption. Then, after completing Step 4, copy or move the backup file to your device.
3. In the File name field, enter a name that will distinguish it from the original tax file (for example, add "Backup" or "Copy" to the file name)
4. Click Save and then close TurboTax.
5. Restart TurboTax and open the backup copy to make sure it's not corrupted. If you get an error, delete the backup and repeat these steps.

If you make changes to your original tax return file, repeat these steps to ensure your original and backup copies are in-synch.

Related Information:                             

• Retrieve a Tax File from a Portable Device
• What's the difference between the tax data file and the PDF file?

AND save it as a PDF so you have access to a copy even if you don’t have the program still installed and operational :

• How do I save my return as a PDF in the TurboTax software for Windows?
• How do I save my return as a PDF in the TurboTax software for Mac?

AND protect the files :

• How can I protect the tax files on my computer?

*** Other clues to the downloaded program ***

In the forms mode ... double click  or right click on a box on a form to data source it ... sadly it doesn't work on all boxes. 

What's the meaning of all the different colors in Forms Mode?

When you look at an onscreen tax form using Forms Mode, you might wonder why one figure is blue and the one next to it is red or black.

These colors indicate the source of that data.