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The standard ros move_base navigation stack already supports what you want to do if you create the proper configuration. First, in move_base, the global_costmap and the local_costmap are completely independent. Second, the global planner never looks at the local_costmap, so changes you make to local_costmap will not affect global planning. Third, you need to research more about costmap_2d and its layered costmap design. Start here:

http://wiki.ros.org/costmap_2d

You can add your own layer and intelligently merge it with the other layers (Obstacle Cost Layer), or you can update the base layer (Static Map Layer). I generally find the former works better.