The Department of Highways shall not change the width, lines or grades of the streets taken over under the provisions of this act or any section thereof but such changes as may be approved or recommended by the Secretary of Highways shall be made by the city as heretofore by an ordinance duly passed in accordance with laws applicable thereto, and in the event of any change of width, lines or grades in accordance with the provisions of this section “and notwithstanding any provisions in the State Highway Law or any other act to the contrary, it is the clear expression of the intent of this act that the Secretary of Highways is authorized, directed and empowered to negotiate with any city of the first class for an equitable allocation and division of costs and responsibilities for the payment of any damages which may be occasioned thereby, such damages to be ascertained and paid in accordance with the laws applicable thereto.”