No, you are not filing an incorrect W-2, you are simply allocating the cash deduction to the correct place. Provided you maintain copies of the documentation, the IRS will not have a problem with it. The hard copy of the W-2 is the documentation.
To qualify for the (Married) $600 cash deduction, you must clear the cash donations from the Schedule A information sheet. That is where the W-2 was trying to put it.
Once that is cleared, the directions from @DoninGA will guide you through the posting process.
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