1. General: "Roofing Solutions: Reference Manual for Property Managers, Owners, Architects, and Specifiers" is an excellent introductory guide to roof maintenance, and effectively explains the bottom line value of a roof maintenance program. It is made available by the GAF Materials Corporation.
2. General: "Life-Cycle Costs of Commercial Roof Systems", a paper formerly available at the website of Carnegie Mellon University's Green Design Institute, provides useful information.
3. General: "Life-Cycle Costing Manual For the Federal Energy Management Program" is a 1995 production of the US Department of Commerce, and well worth reading for its "Introduction to Life-Cycle Cost Analysis".
4. General: "Life-cycle cost analysis (LCCA)" "is a method for assessing the total cost of facility ownership. It takes into account all costs of acquiring, owning, and disposing of a building or building system. LCCA is especially useful when project alternatives that fulfill the same performance requirements, but differ with respect to initial costs and operating costs, have to be compared in order to select the one that maximizes net savings." Basic introduction and very good explanation of the key concepts. Available at the Whole Building Design Guide website.
5. Built-up Roofs: "ROOFER: An Engineered Management System (EMS) for Bituminous Built-Up Roofs" is an extremely detailed and valuable resource put together by the US Army Corps of Engineers' Engineer Research and Development Center. Discussion of the pros and cons of repair vs. replacement starts around page 42 and goes on for some time.