As mentioned, the 2011 Hotfix2 will prevent new corruption, but it cannot fix corrupted scenes or models.
Here’s some tips from Yanick on the Dev team for fixing any models or scenes that you may have.

If you have a corrupted scene:

• In this case you need to load an older version of scene where the shaders are connected, do a New Scene, load the corrupted scene again, and save a clean version of the scene.

If you have a corrupted model, try this to clean it up:

1. Import the model (some materials may be disconnected because the shaders definitions of the ports are not loaded in the same order they were saved)
2. Delete the model again (all the shader definitions are still in the scene)
3. Import the model again (all the shaders are going to be connected because they can find the ports definitions during the load)
4. Export the model again to save the shaders definitions in the right order

PS In 2012, when you load or import corrupted shaders, an error will be logged in the Script Editor. That`s going to make it easier to find corrupted scene/model than looking at materials one by one.