Yes, you are responsible for the $800 franchise filing fee since you did conduct business in California during the year. To prepare your return, you would need to prepare a California and Arizona S-Corp returns. While preparing both State returns, there will be questions in both returns asking you the dates you were doing business in both states so there will be a proper allocation of business activity.
Be sure you prepare your California S-Corp return before completing the Arizona form so that the proper information will flow from/to both states.
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