I got irs refund, then amended to report stock sale. I then owed $1246. Made online payment5/13 and IRS withdrew same amount on 5/15. How do I get 2nd payment refunded?

[johnsomd1958]

How Will IRS reconcile duplicate payment for the 1246 double payment from amended return?

[Critter-3]

The IRS will eventually notice the duplicate payment and refund it ... patience will be needed.  

[fanfare]

@johnsomd1958 

Double check.

You're probably looking at your bank record for your payment.

IRS won't do direct debit on amended tax returns.

[Critter-3]

FYI ...  Along with now allowed efiling of the amended returns you can now also have direct debits but NOT direct deposits.    My professional program allows it so the DIY versions probably do as well. 

So if you efiled the original return and had the balance due debited and you failed to change that option when you completed the FILE tab for the amended return to remove the DD info (or simply understand that the debit would happen)  then it is very possible that a double payment could have happened.   Verify this by reviewing the filing instruction page for the amended return ... is that what happened ?  

[fanfare]

If that's so, the instructions for 1040-X on www.irs.gov need to be updated.

[Critter-3]

Yes they do.  Surprising deposits are not yet allowed.  I was shocked when Drake sent out the notice and I tried one and it worked.