update SkinnedMesh

SkinnedMeshUpdater.cs

using UnityEngine;
using System.Collections;
using System.Collections.Generic;
using UnityEngine.Assertions;
using System;

public class SkinnedMeshUpdater : MonoBehaviour
{
	[SerializeField]
	SkinnedMeshRenderer original;

	#region UNITYC_CALLBACK

	void Update ()
	{
		if (Input.GetKeyDown (KeyCode.Space)) {
			UpdateMeshRenderer (original);
		}
	}

	#if UNITY_EDITOR
	void OnDrawGizmosSelected ()
	{
		var meshrenderer = GetComponentInChildren<SkinnedMeshRenderer> ();
		Vector3 before = meshrenderer.bones [0].position;
		for (int i = 0; i < meshrenderer.bones.Length; i++) {
			Gizmos.DrawLine (meshrenderer.bones [i].position, before);
			UnityEditor.Handles.Label (meshrenderer.bones [i].transform.position, i.ToString ());
			before = meshrenderer.bones [i].position;
		}
	}
	#endif

	#endregion

	public void UpdateMeshRenderer (SkinnedMeshRenderer newMeshRenderer)
	{
		// update mesh
		var meshrenderer = GetComponentInChildren<SkinnedMeshRenderer> ();
		meshrenderer.sharedMesh = newMeshRenderer.sharedMesh;

		Transform[] childrens = transform.GetComponentsInChildren<Transform> (true);

		// sort bones.
		Transform[] bones = new Transform[newMeshRenderer.bones.Length];
		for (int boneOrder = 0; boneOrder < newMeshRenderer.bones.Length; boneOrder++) {
			bones [boneOrder] = Array.Find<Transform> (childrens, c => c.name == newMeshRenderer.bones [boneOrder].name);
		}
		meshrenderer.bones = bones;
	}
}

Nice solution! It works.

same for me, thanks for this code snippet!

works fine thanks a lot

Working great, thanks!

Excellent solution, I had this problem for years.
But you should create a editor script that makes the changes permanent. (Input space not work in editor)