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costmap_updates is an output message of the costmap2D program which is providing updates to just regions that were recently changed instead of sending the full costmap each iteration. It is NOT an input message to change the costmap nor should it be manually set. You should have your updates go through the costmap via plugin layers or other mechanisms to publish out the centralized environmental model.
The fact that you see flickering is because the costmap is overwriting your manually sent changes because the costmap knows nothing about them. Only rviz is using that, nothing else.
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