Apparently both NavMeshes are linked somehow. A NavMesh bake overrides the previous baked avmesh from another scene.
Bug Video
Can’t solve this, I need help.
I’ve tried to delete the cached NavMesh asset from project and regenerate
Deleted all NavMesh data through script
Tried to manually set another fileID to the navmesh
Tried deleting a scene and copying components to a new scene
Tried creating a new project
Ended up solving it.
There’s an option in the project settings called “Enter Play Mode” it makes your game load faster into play mode in exchange for some data reloading.
One of the things it doesn’t reload is static variables (unless told with an argument). All Navmesh data is stored in a static class, therefore it won’t update automatically with this feature enabled.
That’s why if you encounter that problem make sure you have either “Enter Play Mode” to false or that Unity updated their navigation classes and added the Runtime attribute that updates its values.