If you mean the tax owed still shows at the top of the re...

Your tax program sayes we never paid last years taxes however the stat as well as my bank said we did how do we correct this?

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If you mean the tax owed still shows at the top of the return, that will be there forever. This isn't your account, it's the way your tax return looked when it was filed, which is exactly how you should want it. The program has no way to know if you paid your tax or not, since, once you file, payment transactions are between you and the state or the IRS.