Cleanup missing scripts on Prefabs.

CleanupMissingScriptsHelper.cs

using UnityEditor;
using UnityEngine;

public class CleanupMissingScriptsHelper
{
    [MenuItem("Assets/Cleanup Missing Scripts")]
    private static void CleanupMissingScripts()
    {
        foreach (var i in Selection.gameObjects)
        {
            GameObjectUtility.RemoveMonoBehavioursWithMissingScript(i);
            var path = AssetDatabase.GetAssetPath(i);
            var x = (GameObject)PrefabUtility.InstantiatePrefab(i);
            PrefabUtility.UnpackPrefabInstance(x,PrefabUnpackMode.Completely,InteractionMode.AutomatedAction);
            AssetDatabase.DeleteAsset(path);
            PrefabUtility.SaveAsPrefabAsset(x, path);
        }
        AssetDatabase.SaveAssets();
    }
}