Agreed ... if you mailed in the return and later efiled it the IRS can be confused since they are processed by different departments that don't always know what is going on ... a note back to the letter explaining what you did and that the return has been successfully processed and the refund issued will let them close the open issue. If there is a number on the notice you can call you can give them a call or a fax number to send a response is also a valid option.
