The game have to be the same without effects, you can add distorsion, RGBA channel separation that makes you will have millions of colors, but if you deactivate it the game still have to be a two colors game.
You can't use filters to add fade effects or another properties that in two colors is not possible.
No gradient colors, greys or others, with the filters on/off the game have to works in the same way, filters are only applied to the final render image, not to be used as a properti to fade or do something in some sprites.
Hope my explanation was clear :P .