The part of the refund representing amounts paid to the State shall be paid from the county general fund and, when the auditor renders the report which he is required to make to the Controller showing the amount due the State as of the last day of the month preceding the settlement which the county treasurer is required to have with the Controller, the auditor shall certify this amount refunded to the Controller, in the form prescribed by the Controller. On the next settlement of the county treasurer with the State, the Controller, if satisfied of the legality of the refund, shall give the county treasurer credit for the State’s portion of the refund.