After you file

He worked in only one state.
The software says ask for a corrected W-2 and a refund for overpaid taxes (they withdrew too much tax).

If we use only one W2, we don't report all the income and can be audited. Btw, the control numbers are different on these if it matters.
We owe money, so if we get a refund, we'll have to pay it back anyway. The software message seems premature.