After you file

sounds like there was a timing issue with when the letter was created and the check posted.(this happened to me recently as well)

 

Just look at your transcript at IRS.Gov..  See what the balance is.  

 

if there is a credit, I wouldn't even sent back a letter of dispute until mid-July.  Let's see if the refund is issued by then and everuthing zeros out. 

 

what is going to matter is the account balance listed on the transscipt not the letter that is outdated.