The SCRA allows active-duty military members to maintain their legal residence in the place they consider home so you are for all practical purposes, a California resident. California has the "file as a nonresident" rule so that if you are not stationed in California, you do not have to pay state income tax on the active duty pay. However, because you are getting the employer supplement now you do file a California nonresident income tax return. You still do not have to report the Active Duty pay as CA income, so you should get the withholdings refunded. (And if you have not already done so, contact DFAS and request exemption from California withholding while you are stationed outside California.)
Because you are active duty, you are not required to file a Hawaii state income tax return unless you have Hawaii source income outside your active duty pay.
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