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?

[krbauer97]

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.

[Critter-3]

Wait a second ... do NOT file an amended return UNTIL the original return has fully processed.  Until you know what the IRS will do you cannot complete lines 16 or 18 of the 1040X. 

Look at the form 1040X …

Column A should have the figures from the original return, Column C the corrected figures and Column B the differences between the other 2 which needs an explanation on page 2 of the form 1040X.

If you completed it correctly you will see an entry on either line 16 OR 18:

On line 16 should be the amount you paid with your original return. 

On line 18 should be the amount of your original refund you received.

Then you will see your extra refund on line 22 OR  the new balance due you need to pay on line 20.

[xmasbaby0]

"..... I never received it due to an audit. "

No---it is too soon for an audit of a 2019 return, so something else delayed your refund.  Did you receive a letter from the IRS that requested more information or that you verify your identity?  Every letter from the IRS is not a "audit."  What did the letter say?  What numbers were in the top corner?   WHY are you amending your return if it has never been fully processed?  You should not do that or you can cause even more confusion and delay.  Sometimes we see frustrated users who think sending an amended return will shake a refund loose when they are just tired of waiting for a refund.  That does not work.

(what the letters from the IRS mean)

I GOT A LETTER FROM THE IRS   

https://ttlc.intuit.com/questions/3605673-i-got-a-letter-or-notice-from-the-irs