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You probably don't have to do anything. Just wait. The IRS will notice the extra payment and refund it to you. If you don't hear from the IRS after a couple of months, then you will have to contact them.
@rjs - I effectively did the same thing last year..... I have had an amendment sitting in queue for 11 months as a way to flush out the credit due back to me .... doing nothing doesn't appear to automatically refund the payment as it's been 12 months since my duplicate payment and nothing has been refunded.
You did not do nothing. You filed an amended return. I suspect that the amended return is what is holding up your refund. The IRS knows that you have an amended return in the pipeline, that has not been processed yet. They are not going to send you any money until they see what effect the amended return has. If you had simply waited, I think you would have gotten your money back by now. Your experience is not the same as doing nothing and waiting, because you filed the amended return.
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