It depends. Usually, it does not. If you are to receive a refund and end up owing after the audit, they can deduct the amount you owe from your refund, but only if you do not receive your refund before the audit. However, if you owe nothing after the audit, again, you will receive your refund. But it is difficult to say exactly what will happen, it all depends on the IRS or the State, whoever sent the notice of the audit.
