The next generation hadron accelerators will operate with MW beams or store beams with an energy of many 100 MJ. Such accelerators must be protected by fast and very reliable interlock systems to avoid damage due to uncontrolled beam loss. Machine protection will constrain operation, but some operational flexibility is still required for commissioning and performance optimization. This is a substantial challenge for control systems and application programs. New tools are developed to face those challenges: critical settings management, software interlocks, role based access to equipment, automatic accelerator mode recognition etc. This talk presents some of the challenges and tools. Experience with novel approaches are discussed
