Not only does it change if you update at runtime, it also changes if you update it period.
I’m not updating the navmesh at runtime, and I set the Agent Radius in my Project Settings to be 200, but after closing the project and reopening, The radius did not update. I then manually set the Agent Radius in the RecastNavMesh-Default actor in the world outliner, and this DID update the value, however, upon restarting the project, the values were reset back to the defaults.
This issue is happening in UE 5.3 - I’m going to submit a new report since I just realized this thread is 9 years old.