I e-filed a 2022 amended federal return for a client in mid-April, 2023, to declare additional investment income that had been overlooked on the original return.  On the original return, the client also chose to have his 2023 estimated tax payments electronically withdrawn, so the boxes for each payment were checked in Part III of 1040-ES.  Today my client informed me that both the first and second quarter 2023 estimated tax payments were withdrawn twice; same exact amounts on the same exact dates. 

It is just a guess on my part, but the only thing I can think that might have caused this to happen was that on the amended return I never unchecked any of the boxes in Part III of 1040-ES pertaining to the electronic payment of estimated tax.  Since none of the information on the 1040-ES was being changed in the amended return, it never dawned on me that such a change would be necessary.  I never even knew such a change was possible to accomplish with an amended return.

Has anyone else experienced this?  Should I have unchecked the authorization for electronic payment of estimated taxes on the amended return, or was this a mistake made by IRS?  This is just my latest headache with amended returns. 😅

Many thanks for any input.

Mike