No, the program won't e-file your original return twice.
You can e-file your tax return, amend your return, and e-file the amended return.
So, the question now is did you amend your return, or did you just change something?
If you simply changed your return after it is e-filed and accepted, without starting an amended return, it just sits there. Nothing is changed with the IRS.
If you started an amended return because you needed to make a correction, and you selected Amend (change) return before making your changes, you need to file your amended return. You can print and mail it, or submit it for e-file.
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