If the Controller believes or has reason to believe that the payment of any portion of the omnibus claim appropriation may violate the provisions of the Constitution, he shall withhold payment of the questioned portion and shall issue his warrant for the remainder of the appropriation. The secretary, subject to the board’s approval, shall promptly disburse the undisputed portion of the omnibus claim appropriation and shall promptly give notice to the Joint Legislative Budget Committee of the Controller’s action concerning the withheld portion.