A client of mine received a notice that he didn’t  pay the total balance that was due on his tax return. Yet, the amount that he paid was equal to his 8879, the balance due on the return, and every e-file status or acknowledgment that I could find in LaCerte. 
I’m not sure how to proceed. If I knew what values were on the strange incorrect version the IRS received, I would do an amended return; but I don’t know what is on the version they have. 
Thoughts and assistance are greatly appreciated.