The W-2 will not make a difference because the law is very straight forward, which is CA does not conform to IRC for HSA.  Did the notice not propose the changes and compute the additional tax?  If so, you should just need to check the proposed changes and agree to them if you and your client are in agreement.

If you had entered Code W as George explained, the HSA amount should flow to Schedule CA (540) Line 7, Column C to increase the state taxable income for wages.