I think you mean you were due a refund on your original tax return that was filed but you have not received it. You then amended the return and ended up owing taxes, so you paid the balance due. So now you don't know what will happen to the refund you never received.
If so, you just need to wait, as the IRS should send you the refund amount. It is probably just being held up, maybe because of the issue with your tax return needing to be amended.
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