Need to save a Maya scene but without saving a reference

I have a scene with a helper node in it that is referenced into the scene. It is brought in by a tool. However when the user saves a file, I don’t want this help node reference saved into this file. Other than unloading the reference, saving the scene, and re referencing, How would you do this? I am on Maya 2014 and writing in Python.

MO

http://download.autodesk.com/global/docs/mayasdk2012/en_us/index.html?url=cpp_ref/class_m_scene_message.html,topicNumber=cpp_ref_class_m_scene_message_html

use the mscenemessage functions to add a callback with kBeforeSave message, then you can decide what to do with your reference bevore the file is actually written, maybe delete it, or import the reference?