I recently submitted a 1040x for a client that had automatic estimated quarterly payments set up for the IRS in the return. I was unaware that I needed to unmark those estimated payments prior to efiling an amended return . As a result, the client is now having estimated payments pulled twice.
I suggest the programmers create a way to cross check that before you efile to prevent issues like this from happening. Maybe make the items red so you have to confirm you want to submit the automatic estimated quarterly payments again on a 1040x.
Update; I just prepared a 1040X for a return that I had setup ACH ES payments for 2024 with ProSeries. I create a duplicate copy of the original return and prepare the 1040X.
When I activated the 1040X and made the appropriate changes I received (red) errors on the "X's" for automated 1040ES payments. Once I removed the X's everything was fine and there's No chance that there will be duplicate ES payments.