A quick hack to clone a Three.js GLTF scene without re-loading or re-parsing the source.

three-clone-gltf.js

const cloneGltf = (gltf) => {
  const clone = {
    animations: gltf.animations,
    scene: gltf.scene.clone(true)
  };

  const skinnedMeshes = {};

  gltf.scene.traverse(node => {
    if (node.isSkinnedMesh) {
      skinnedMeshes[node.name] = node;
    }
  });

  const cloneBones = {};
  const cloneSkinnedMeshes = {};

  clone.scene.traverse(node => {
    if (node.isBone) {
      cloneBones[node.name] = node;
    }

    if (node.isSkinnedMesh) {
      cloneSkinnedMeshes[node.name] = node;
    }
  });

  for (let name in skinnedMeshes) {
    const skinnedMesh = skinnedMeshes[name];
    const skeleton = skinnedMesh.skeleton;
    const cloneSkinnedMesh = cloneSkinnedMeshes[name];

    const orderedCloneBones = [];

    for (let i = 0; i < skeleton.bones.length; ++i) {
      const cloneBone = cloneBones[skeleton.bones[i].name];
      orderedCloneBones.push(cloneBone);
    }

    cloneSkinnedMesh.bind(
        new Skeleton(orderedCloneBones, skeleton.boneInverses),
        cloneSkinnedMesh.matrixWorld);
  }

  return clone;
}

I didn't need this, and used gltf.scene.scale.set instead which is much simpler:

const loader = new GLTFLoader();
        const tree = await loader.loadAsync("objects/Tree_1.gltf");
        const treeScale = 0.2;
        tree.scene.scale.set(treeScale, treeScale, treeScale);