My accepted return shows a refund. My amended return will show a balance due. Should I file the amended return before my refund arrives?

Because of a late arrived 1099, I must report additional income.  It results in a balance due rather than a refund.  I don't wish to trigger an audit by receiving a refund I am not entitled to.  I would immediately send in payment of the unearned refund plus toe income related tax liability, but do not wish to run the risk of the IRS initiating an audit because of this.