I need to update return after receiving a letter from IRS, date had passed. I amended, now seeing I shouldn't have. How do I update the original refund so I dont overpay?

My mail had been on hold, so the due date to respond had passed. It has been 2.5 months without a return (original or adjusted from IRS). I went ahead and amended the return, not realizing that was wrong. Now I am paying what I owe plus what they think I was refunded. But I was not refunded. How to I move forward? Will the IRS catch the 'overpayment' before adjusting the refund down? If they do adfjust down, is there recourse?

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