PropTools.cs

using UnityEditor;
using UnityEngine.SceneManagement;

public class PropTools {

    [MenuItem("Edit/Custom/Save All Prefabs")]
    public static void SaveAllRootPrefabs()
    {
        var roots = SceneManager.GetActiveScene().GetRootGameObjects();
        for (var i = 0; i < roots.Length; i++)
        {
            var root = roots[i];
            var perc = i / (float) roots.Length;
            var type = PrefabUtility.GetPrefabType(root);
            if (type == PrefabType.PrefabInstance || type == PrefabType.DisconnectedPrefabInstance)
            {
                var prefab = PrefabUtility.GetPrefabParent(root);
                EditorUtility.DisplayProgressBar("Saving all prefabs...", "Saving " + root.name, perc);
                PrefabUtility.ReplacePrefab(root, prefab, ReplacePrefabOptions.ConnectToPrefab);
            }
        }
        EditorUtility.ClearProgressBar();
    }
}