GraphUpdateScene effect disappears after some time

I am using GraphUpdateScene with NavMesh. The effect of it disappears after sometime. Scan button in the editor works fine, but the Scan() method doesn’t count the GraphUpdateScene scripts in. This works just as intended with HexagonGraph tho. But due to some stuff I would prefer using the NavMesh over the Hexagon Grid. Is there a way to make the NavMesh changes not disappear?

Video with example: