Super userful script for applying changes to multiple prefabs. Simply highlight prefabs, go to GameObject menu and select 'Apply Changes To Selected Prefabs'

ApplySelectedPrefabs.cs

// --------------------------------------------------------------------------------------------------------------------
// <copyright file="ApplySelectedPrefabs.cs" company="Supyrb">
//   Copyright (c) 2017 Supyrb. All rights reserved.
// </copyright>
// <author>
//   baptisteLar
//   http://baptistelargaiolli.com/
// </author>
// <author>
//   Johannes Deml
//   send@johannesdeml.com
// </author>
// --------------------------------------------------------------------------------------------------------------------
 
namespace Supyrb.EditorTools
{
    using UnityEditor;
    using UnityEngine;
 
    /// <summary>
        /// Apply or revert multiple prefabs at the same time
        /// Source: https://forum.unity3d.com/threads/little-script-apply-and-revert-several-prefab-at-once.295311/
        /// </summary>
    public class ApplySelectedPrefabs
    {
        private delegate void ChangePrefab(GameObject go);
        private const int SelectionThresholdForProgressBar = 20;
        private static bool showProgressBar;
        private static int changedObjectsCount;
 
        [MenuItem("GameObject/Apply Changes To Selected Prefabs %j", false, 100)]
        private static void ApplyPrefabs()
        {
            SearchPrefabConnections(ApplyToSelectedPrefabs);
        }
 
        [MenuItem("GameObject/Revert Changes Of Selected Prefabs", false, 100)]
        private static void ResetPrefabs()
        {
            SearchPrefabConnections(RevertToSelectedPrefabs);
        }
 
        [MenuItem("GameObject/Apply Changes To Selected Prefabs", true)]
        [MenuItem("GameObject/Revert Changes Of Selected Prefabs", true)]
        private static bool IsSceneObjectSelected()
        {
            return Selection.activeTransform != null;
        }
 
        //Look for connections
        private static void SearchPrefabConnections(ChangePrefab changePrefabAction)
        {
            GameObject[] selectedTransforms = Selection.gameObjects;
            int numberOfTransforms = selectedTransforms.Length;
            showProgressBar = numberOfTransforms >= SelectionThresholdForProgressBar;
            changedObjectsCount = 0;
            //Iterate through all the selected gameobjects
            try
            {
                for (int i = 0; i < numberOfTransforms; i++)
                {
                    var go = selectedTransforms[i];
                    if (showProgressBar)
                    {
                        EditorUtility.DisplayProgressBar("Update prefabs", "Updating prefab " + go.name + " (" + i + "/" + numberOfTransforms + ")",
                          (float)i / (float)numberOfTransforms);
                    }
                    IterateThroughObjectTree(changePrefabAction, go);
                }
            }
            finally
            {
                if (showProgressBar)
                {
                    EditorUtility.ClearProgressBar();
                }
                Debug.LogFormat("{0} Prefab(s) updated", changedObjectsCount);
            }
        }
 
        private static void IterateThroughObjectTree(ChangePrefab changePrefabAction, GameObject go)
        {
            var prefabType = PrefabUtility.GetPrefabType(go);
            //Is the selected gameobject a prefab?
            if (prefabType == PrefabType.PrefabInstance || prefabType == PrefabType.DisconnectedPrefabInstance)
            {
                var prefabRoot = PrefabUtility.FindRootGameObjectWithSameParentPrefab(go);
                if (prefabRoot != null)
                {
                    changePrefabAction(prefabRoot);
                    changedObjectsCount++;
                    return;
                }
            }
            // If not a prefab, go through all children
            var transform = go.transform;
            var children = transform.childCount;
            for (int i = 0; i < children; i++)
            {
                var childGo = transform.GetChild(i).gameObject;
                IterateThroughObjectTree(changePrefabAction, childGo);
            }
        }
 
        //Apply    
        private static void ApplyToSelectedPrefabs(GameObject go)
        {
            var prefabAsset = PrefabUtility.GetCorrespondingObjectFromSource(go);
            if (prefabAsset == null)
            {
                return;
            }
            PrefabUtility.ReplacePrefab(go, prefabAsset, ReplacePrefabOptions.ConnectToPrefab);
        }
 
        //Revert
        private static void RevertToSelectedPrefabs(GameObject go)
        {
            PrefabUtility.ReconnectToLastPrefab(go);
            PrefabUtility.RevertPrefabInstance(go);
        }
    }
}