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After studying the code of costmap_2d::VoxelLayer I found the reason why.

Apparently, the clearing strategy implemented in the VoxelLayer works fine, however, when the points in the clouds that don't lie in the range min/max_obstacle_range are removed from the observation set so, for instance, if you set a min_obstacle_height to filter the floor, the observation of the floor are removed and no clearing is applied.