California and Mississippi will match the income reported in Box 16 against their records (they get a W-2 from your employer). You may have problems if you use the Box 1 amount since CA and MS wages are clearly stated on your W-2.
Ideally your company should issue a corrected W-2. Sounds like they won’t do that.
The alternative is to report the CA and MS wages as shown on your W-2 and take a tax credit on your MS return for tax paid to California. This is easy to figure because the credit would be based on your entire CA income and tax liability.
Your third option would be to use Box 1 and respond to tax notices if you get audited.
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