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Instead of running two separate instances of move_base, why not write your own BaseGlobalPlanner that is essentially a supervisor for navfn and the carrot planner? This supervisory planner could have instances of both planners you want to switch between and can implement the logic required to know when to switch, then forward any of standard calls move_base makes (such as the call to make a plan) to the appropriate planner. Then just have a single instance of move_base load up your supervisory planner.