Thats the reason, because the material is completely new and of other kind you should change the material to the mesh.
mesh.material = myNewMaterial
You should traverse the scene
const myNewMaterial = new THREE.MeshPhysicalMaterial({
metalness: 1,
roughness: 0,
transparent: true,
opacity: 0.5,
envMapIntensity: 1,
side: THREE.FrontSide, // to test change this to `THREE.DoubleSide` just in case.
color: 0x000000 // do not forget to set the right color to the new material.
});
scene.traverse((obj) => {
if(obj.isMesh && (obj.material.name.includes('Glass') || obj.material.name.includes('GLASS'))) {
obj.material = myNewMaterial;
}
})