You don't need to change the returns. Since you were married before the end of the year, and your spouse has lived in California since the latter part of the year, you can file a joint Nonresident return for New York and joint Resident return for California.
New York has one form, Form IT-203, Nonresident and Part-Year Resident Income Tax Return, that covers taxpayers who were nonresidents either part or all of the year. See this New York webpage for more information.
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