Are you saying that you got a letter from the IRS (like a CP2000) reporting that you owe tax from a prior year?
The process of handling these "letter audits" (as the IRS calls them) is separate from the e-filing and refund process.
This means that while the IRS has the right to take any refund to pay any money that you owe, they won't until the letter audit process is completed (you have to reply to this letter, correct?) by which point your refund from your already e-filed return will have probably already arrived to you.
