I was afraid of that, Ive been unchecking those ES withdrawal boxes when transmitting amended returns.   Just in case it was sending that info again with the amended return. 

I uncheck all the Electronic payment boxes with amended returns, I just dont trust the program, doesnt have enough communication or verification processes to show me whats actually going to happen, I make any amended return payments directly on the tax agency websites.

I hope it didnt put your client in a bad situation with their bank account, and maybe now you can call and cancel the 3rd and 4th ES payments, they should be all paid up?   The number to cancel the payments is right on the Form 8879.  Have the bank account info on hand when you call.