To reproduce:
1. Create a cube
2. Open the animation window
3. Add a curve for the cube - select Mesh Renderer > Material._Color
4. Remove the Material._Color.r, Material._Color.g, Material._Color.b properties
5. Notice how the cube in the animation is now black - the color properties defaulted to 0

It is caused by the removal of the other color properties(rgb). This can be workarounded by animating the Material._Color without removing any properties and just editing the alpha curve.