First the friend ... the IRS must have gotten a 1099-S reporting the sale so that is why they got a letter. Those forms are included in the closing docs you get and are not mailed in January like other reporting forms.
As for you ... the amended return you mailed in earlier this year will required at least 6 months to process probably longer ... do NOT send in anything else at this time. When you eventually get the IRS notice you can simply respond with the facts of the sale showing the profit was excludable ... may not need another amended return for just this so call the number on the notice to see how they want it handled.
