This sounds like a case (unfortunately) where you just need to wait for the IRS to post the payment for what you owe ($1300) then the rest will be refunded. The Taxpayer Advocate is your best source for getting the rest of the refund id there is a delay- but even they must wait a "reasonable" time (and reasonable for IRS is slow in real life). The best I can say is wait a week and call again if you do not have your refund- as soon as the payment for the amount owed is posted, the refund will be issued.
@singlemom1982
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