Hi there,
Because the Mesh is generated at runtime, there will not be a reference to it between loads because it won't exist. Instead you will need to save it directly.
To save the Mesh you need to save the mesh of the MeshFilter, rather than trying to save a Mesh component. I.e.
ES3.Save<Mesh>(this.gameObject.name, this.gameObject.GetComponent<MeshFilter>().sharedMesh, "MeshFolder.es3");
All the best,
Joel