Fix Masks

//saves you from agonizing manual clicking "Fix Mask" on each user-created clip,
//when you have updated/edited the original FBX changing the skeleton hierarchy

//drop this in your Scripts/Editor folder,
//select FBX's and right click context menu Fix Animation Masks
//tested on Unity 4.7

//minor update, sets all transforms of the avatarMask to active (assuming you are just using 'Mask Definition Create From This Model' with all transforms active (Default behavior)

using UnityEditor;
using UnityEditorInternal;
using UnityEngine;
using System;
using System.Reflection;

public class FixMask
{
	[MenuItem("Assets/Fix Animation Masks")]
	private static void Init()
	{
		UnityEngine.Object[] selection = Selection.GetFiltered(typeof(UnityEngine.Object), SelectionMode.DeepAssets);
		foreach( UnityEngine.Object obj in selection )
		{
			string path = AssetDatabase.GetAssetPath( obj );
			ModelImporter mi = AssetImporter.GetAtPath(path) as ModelImporter;

			Type modelImporterType = typeof(ModelImporter);

			MethodInfo updateTransformMaskMethodInfo = modelImporterType.GetMethod("UpdateTransformMask", BindingFlags.NonPublic | BindingFlags.Static);

			ModelImporterClipAnimation[] clipAnimations = mi.clipAnimations;
			SerializedObject so = new SerializedObject(mi);
			SerializedProperty clips = so.FindProperty("m_ClipAnimations");

			AvatarMask avatarMask = new AvatarMask();
			avatarMask.transformCount = mi.transformPaths.Length;
			for( int i=0; i<mi.transformPaths.Length; i++ )
			{
				avatarMask.SetTransformPath(i,mi.transformPaths[i]);
				avatarMask.SetTransformActive(i,true);
			}

			for( int i=0; i<clipAnimations.Length; i++ )
			{
				SerializedProperty transformMaskProperty = clips.GetArrayElementAtIndex(i).FindPropertyRelative("transformMask");
				updateTransformMaskMethodInfo.Invoke(mi, new System.Object[]{avatarMask, transformMaskProperty});
			}
			so.ApplyModifiedProperties();

			AssetDatabase.ImportAsset(path);
		}
	}
}