How can I correct the IRS form automatically taking the estimates from both superceded and original returns

Close the bank account before they get there. 

you may be able to make adjustments by having TP create an IRS account 

Paper file?

Let the client take care of estimate payments instead of you doing it through the software?

Yea, I got schooled in that mistake last year with 2 or 3 different clients, what a hassle for my oversight!

You can call the phone number on the 8879 and cancel all rest of the doubled up payments, have the clients info and banking info on hand, you'll need it. be sure you tell them it was an EFILE payment, not EFTPS, they look at EFTPS at first and wont be able to find it, the key word is EFILE payment!

Sadly, you wont be able to get the double payment refunded.  

Sorry to hear.  I had this happen too.  My client was understanding but also would still like to know why!  Has anyone discovered an override or place to put in "replace prior estimates?"  While I'm now aware and hopeful it doesn't come up again, I still wonder if there was something I could have done (other than call EFPTS before 4/15) when I filed the superceded return so the second set of estimates would not have happened.

Thanks,

Colleen