Yes, you leave the W-2s as is when filing Form 843. You should consider sending a letter of explanation or have the 'Agent for' payroll company provide a letter of explanation for you to send to the IRS.
As indicated above, you can use the TurboTax CD/Download version to make correction to the original return if you choose. You should mail the return and include the W-2s and letter when mailing your tax return. No Form 843 is required in this situation. The timing may actually be faster if you e-file and then send Form 843.
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