OK ... first the IRS is underfunded and understaffed so only 7% (or less) of the calls ever get answered.
Now did you get a balance due letter from them ? If so simply mail back proof of payment with the notice with a short, polite note stating the payment had already been made.
If you have not yet gotten a notice then just hang in their. Returns with balance dues on them are on the very back burner while they process returns with refunds on them first. Eventually they will process your return and the payment should be accounted for automatically.
