Thanks to Wu Yunze for part of the code.Unity batch modification prefab
Thanks to Lin Xinfa’s part of the code.Unity3D editor: delete the MissingScirpt script

Problem: I used prefabs from other places, but I dropped their scripts (their scripts are not suitable for myself). When instantiating this Prefab, I will print a lot of warning messages under the Editor. This message will affect the loading efficiency. Slow loading speed, and even cause a crash (in the packaged out to load Bundle through UnityWebRequest no problem, instant crash when instantiation), some students will say, I manually deleted it, but the prefab of productization is often relatively large, The structure is relatively complex, and there may be hundreds or thousands of nodes that lose scripts.

Requirement: Clean up all missing scripts in the prefab in the specified directory (recursive cleanup, including hidden nodes, clean up and write back to prefab)

Establish a test environment:
The first step is to create an empty scene, add the root node G1, add two child nodes Child1 Child2 and attach a new C# script NewBehaviourScript.cs, then hide Child1 and store G1 as Prefab

The second step is to delete NewBehaviourScript.cs Apply Prefab: G1

Ok, here is the environment, the following is the Editor code.

  [MenuItem("Tools/clean up missing scripts in prefab")]
    public static void RMLosedComponentInPrefab()
    {
        EditorUtility.DisplayProgressBar("Modify Prefab", "Please wait...", 0);
        string[] ids = AssetDatabase.FindAssets("t:Prefab", new string[] { "Assets/data/testLoseScript" });
        for (int i = 0; i < ids.Length; i++)
        {
            string path = AssetDatabase.GUIDToAssetPath(ids[i]);
            GameObject prefab = AssetDatabase.LoadAssetAtPath(path, typeof(GameObject)) as GameObject;
            GameObject instance = PrefabUtility.InstantiatePrefab(prefab) as GameObject;

            int delCount = 0;
            RecersiceModifyGameObject(instance, ref delCount);

            if (delCount > 0)
            {
                Debug.Log(instance.name + " remove losed:---- " + delCount);
                // save 
                PrefabUtility.ReplacePrefab(instance, prefab, ReplacePrefabOptions.ConnectToPrefab);
            }
            UnityEngine.Object.DestroyImmediate(instance);
            EditorUtility.DisplayProgressBar("Modify Prefab", "Please wait...", i / (float)ids.Length);
        }
        AssetDatabase.SaveAssets();
        EditorUtility.ClearProgressBar();
    }

    private static void RecersiceModifyGameObject(GameObject obj, ref int delCount)
    {
        //find child
        if (obj.transform.childCount > 0)
        {
            for (int i = 0; i < obj.transform.childCount; i++)
            {
                var _childObj = obj.transform.GetChild(i).gameObject;
                // modify this GameObject
                RecersiceModifyGameObject(_childObj, ref delCount);
            }
        }
        // change instance 
        SerializedObject so = new SerializedObject(obj);
        var soProperties = so.FindProperty("m_Component");
        var components = obj.GetComponents<Component>();
        int propertyIndex = 0;
        int innerDelCount = 0;
        foreach (var c in components)
        {
            if (c == null)
            {
                ++delCount;
                ++innerDelCount;
                soProperties.DeleteArrayElementAtIndex(propertyIndex);
            }
            ++propertyIndex;
        }

        if (innerDelCount > 0)
            so.ApplyModifiedProperties();
    }

result:
After the cleanup is done like this