I filed an amended return that says I owe the IRS $991. My refund was supposed to be $5,000 and I never received it due to an audit. Will they take it out of the refund?

It says I have to mail a check or pay by debit but they still owe me the difference of $4,010 so I do not want to mail the check in fear of not getting the balance. I have been waiting to hear back from someone since March.