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octomap_server is a standalone node belonging to octomap_ros that is completely independent of moveit. The octomap library is used inside moveit (or more precise, the move_group node) for representing environment geometry, but that does not mean that loading a octomap into octomap_server automatically makes it known to moveit.
One option to feed the octomap to moveit is using the planning scene ROS API described in this tutorial. Using that you can send new octomap collision geometry to moveit as part of the moveit_msgs/PlanningSceneWorld message inside the moveit_msgs/PlanningScene message.
Another (perhaps easier) option is to update the internal moveit octomap directly using your sensors, see moveit 3D Perception/Configuration.
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