Original report by CS (Bitbucket: optimisez, GitHub: optimisez).
When you update the PrefabBuilder script, for example, add box collider component it will not update the prefab with box collider component attached after pressing build button for second times. The current workaround is to change the SerializeField variable from Create Prefab From Group node each time to notify AssetBundleGraph that the prefab needs to update. Seems like there are no mechanics currently to detect the new changes of updated PrefabBuilder script.