RemoveMissingComponentsInCurrentScene.cs

    private static void RemoveMissingComponentsInCurrentScene(ILevelData levelData)
    {
        var badComponents = SceneManager
            .GetActiveScene()
            .GetRootGameObjects()
            .Flatten()
            .Select(gameObject => new
            {
                GameObject = gameObject,
                Components = gameObject.GetComponents<Component>()
                    .Select((c, i) => new {Component = c, Index = i})
                    .Where(componentIndex => componentIndex.Component == null)
                    .ToList()
            })
            .Where(gameObjectComponents => gameObjectComponents.Components.Any())
            .ToList();

        foreach (var gameObjectComponents in badComponents)
        {
            var serializedObject = new SerializedObject(gameObjectComponents.GameObject);
            var prop = serializedObject.FindProperty("m_Component");
            gameObjectComponents.Components
                .Select(_ => _.Index)
                .OrderByDescending(x => x)
                .ForEach(i => prop.DeleteArrayElementAtIndex(i));
            serializedObject.ApplyModifiedProperties();

            EditorUtility.SetDirty(gameObjectComponents.GameObject);
            EditorSceneManager.MarkSceneDirty(gameObjectComponents.GameObject.scene);
        }

        if (badComponents.Any())
        {
            Debug.Log("Updating scene " + levelData.Scene);
            EditorSceneManager.SaveOpenScenes();
        }
    }