You can't change the box 16 amounts on your own. Since your employer won't change them, the simplest thing for you to do is just file the way the employer reported it.
The California Franchise Tax Board (FTB) is very aggressive about collecting every cent of income tax that they think you owe. If you report less California income than what your W-2 shows, you will end up having to try to convince the FTB that the W-2 is wrong. Since your employer does not agree, that will be very difficult.
