シーン中のすべての Prefab を Revert / Apply する

using Unity.Linq;
using UnityEditor;
using UnityEngine;
using UnityEngine.SceneManagement;

public class AllPrefabEdit
{
    [MenuItem("Tools/Edit/Revert All Prefab Instances %F1")]
    public static void RevertAllPrefabInstances()
    {
        foreach (var rootObj in SceneManager.GetActiveScene().GetRootGameObjects())
        {
            foreach (var obj in rootObj.DescendantsAndSelf())
            {
                if (PrefabUtility.IsAnyPrefabInstanceRoot(obj))
                {
                    PrefabUtility.RevertPrefabInstance(obj, InteractionMode.AutomatedAction);

                    Debug.Log($"Revert succeeded: {obj.name}");
                }
            }
        }
    }

    [MenuItem("Tools/Edit/Apply All Prefab Instances %F2")]
    public static void ApplyAllPrefabInstances()
    {
        foreach (var rootObj in SceneManager.GetActiveScene().GetRootGameObjects())
        {
            foreach (var obj in rootObj.DescendantsAndSelf())
            {
                if (PrefabUtility.IsAnyPrefabInstanceRoot(obj))
                {
                    PrefabUtility.ApplyPrefabInstance(obj, InteractionMode.AutomatedAction);

                    Debug.Log($"Apply succeeded: {obj.name}");
                }
            }
        }
    }
}

メニューの Tools > Edit か、Ctrl+F1, Ctrl+F2 で実行できます。

※ LINQ to GameObject が必要です。