If you’re still having problems with disconnected shaders, even with HotFix2, you could try using dotXSI to remove any corrupt materials from your material library.
Here’s the basic procedure. You may want to create a temporary copy of your material library, and then use the explorer to copy all the materials into the temporary material library.
- Load the original asset (scene or model).
- In the explorer, switch to Materials scope, and click the icon for the material library.
- In the library PPG, change the storage to External (dotxsi text) and click Export Library.
- Save the scene.
- Close and restart Softimage.
- Open the scene.
- In the explorer, right-click the material library and click Locks > Unlock All Levels.
- In the material library PPG, change the storage back to Internal.
- Save or export the asset.
eX-SI 
This solution seem to fix the problem temporarily.
If I use this solution to clean up a material library then save my scene, no warning or errors are displayed.
But if your export the model, import it back as reference in another scene then make the model local, a bunch of warning appears again.
These warning are a bit scary because you know your scene will lose it’s shaders at some point.
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You can get a partial automation for this here:
http://www.softimageblog.com/archives/590