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After you file
In the Desktop program all you have to do is go to Forms mode and delete the 1040X. Then take the changes out.
How to delete an Amended return in the Desktop program,
Did you have trouble efiling it? I have seen posts from people saying they can't efile the amended return from the Desktop program. To amend in the Desktop program.....
First you need to update your return with the filing status so it knows it was filed and accepted. For the Desktop program you have to check the filing status inside the program.
Open your return and go up to menu item
File > Electronic Filing > Check Electronic Filing Status
Then save your return and close and reopen it.
And before you amend you should have saved a copy of your file so you have the original. Go up to File-Save As and give it another name.