In connection with any proceeding involving a public utility with a net investment of $1,000,000 or more, the expenses of any investigation or proceeding of any nature by the Commission of or concerning any public utility operating in the Virgin Islands, and all expenses of any litigation, including appeals, arising from any such investigation, valuation, revaluation, or proceeding, or from any order or action of the said Commission, shall be borne by the public utility investigated, or otherwise affected as a special franchise tax in addition to all other taxes imposed by law, and such expenses with interest at 6 per centum per annum may be charged to operating expenses and amortized over such period as the Commission shall deem proper and be allowed for in the rates to be charged by such utility except any cost or expenses associated with any investigation or proceedings regarding the certification or interconnection of a “Qualifying Cogeneration Facility or, Qualifying Small Power Production Facility”, as defined in 30 V.I.C., § 46, is governed solely by 30 V.I.C., §§ 47 and 48. When any such investigation, or other proceeding is begun the said Commission may call upon the utility in question for the deposit of such reasonable sum or sums as in the opinion of said Commission, it may deem necessary from time to time, until the said proceeding or the litigation arising therefrom is completed, the money so paid to be deposited in the Treasury of the Virgin Islands in a special account to be maintained and administered by the Commissioner of Finance and to be designated the “Special Public Utility Deposit Account”; provided, that the amount so assessed by the Commission to any one company in any one year, in any rate case shall not exceed one-half of one per centum of the existing net investment of the company investigated, and that the amount so assessed in all other investigations shall not exceed one-tenth of one per centum of the existing net investment.