I came across a blog a few days ago that had a small little script that basically goes through your entire max scene and deletes all materials. It appears it goes thru your scene and remove every material from every single object in your scene. However it leaves your material balls perfectly intact!
So here is how I have worked it into my workflow.
1) I installed the script into my Max GUI as a button. Will show you how to do that later!! (The original site suggested just typing it into the MAXScript listener, however I use it a lot)
* My standard method when working with Materials is never to delete used materials from the Material Editor, thus with this system your materials will be safe!
2) Run the script! Simply by clicking the newly created button. This will remove every material applied to every object in the scene. All objects will revert to their original base ‘max colour’.
3) Now carefully and only selecting the meshes that require materials applied, you re-apply the material balls from the Material Editor
* I normally only ever use a single material ball with a Multi/Sub-Object. This allows me to use Material IDs to apply materials, so re-applying a single material ball to a scene is a breeze!
4) Its now simply a matter of saving your new clean scene.
* I would just for safety sake save it under a new name, just in case or until you trust the system!
That should have completely cleaned your scene of any missing or untraceable materials or texture files!
Installing & Creating the Max Script Button
1) Firstly download the script file. Here!!
2) Unzip the script into your ‘3ds Max\Scripts\’ folder
3) Open Max, and click the ‘Utilities’ tab, then click the ‘MAXScript’ button.
4) Click ‘Open Script’ then browse to and open ‘Clear All Materials.ms’
5) This will launch the MAXScipt Listener with the script inside. Now simply select all the text in the window and Drag it onto any tool bar along the top of the screen (Once you drop it, it will create a button for you!)
6) If you would like, you can right click the button to edit its details and appearance.