You can autokey the material changes you make. First 50 keys white and next 50 black. At least that is the first thing that comes to mind. Something like this [ame="http://www.youtube.com/watch?v=Ka2LChUzBiA"]3d Max tutorial: Creating animated textures - YouTube[/ame]
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@mAlkAv!An: Thank you, good sir. I was able to use your method to do some crazy material swaps.