What’s going on is that there are navmesh values also in your project settings, and those are overwriting the values in your navmesh in your level whenever you restart Unreal.
Go to Edit > Project Settings > Engine > Navigation Mesh
Change the values in the project settings to the ones you want, and they’ll overwrite the values in the navmesh in your level and won’t go back after restart. I’d love an explanation why these values in particular work like this, if anyone knows.