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Add the amount paid after filing to the extension payment in the TT program ...
To enter, change or delete a payment made with an extension request (Federal, State, Local) -
On the next screen select the type of extension payment made and click on the start or update button
Or enter federal extension payment in the Search box located in the upper right of the program screen. Click on Jump to federal extension payment
We hope your procedure will propagate such a revision to Form 1040-X if an AMEND is in progress.
It should.
You can't use this procedure if you are e-Filing (now closed) because you will be
changing the "payment with extension" line. That's not what the OP said.
When paper filing 1040-X,
do not include your old 1040 nor your revised 1040 because the Form 1040-X reflects any changes there and becomes your new tax return.
If the program thinks you sent the entire payment then you may not be able to change this in the program so you may need to manually change line 16 and the rest of the return as well. Or you can file it as is just knowing you did not send the full payment and either send what you really do owe now or wait for what should be a refund as the IRS will automatically recompute the bottom line for you.
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