@coolbean --
As I said previously, I don't think you need to file amended returns if your original return allocated your income correctly. I might also mention that neither Illinois nor California have separate tax forms for part-year residents. CA uses Form 540NR for both non-residents and part-year residents. Illinois uses Form IL-1040 with Schedule NR in both cases.
I don't think Illinois is disputing the numbers on your returns. It sounds like they simply want proof that you actually did move to California on the dates you claimed. Since your employer unfortunately is not willing to help you, my suggestion would be that you appeal the Illinois decision in writing and ask them what forms of proof they will accept in place of an employer letter which you are unable to obtain. The laws of both states are on your side.
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
