You don't need to convert the material, and it's important that you don't, because what happens is that while exporting each frame, the plugin will ask the Cinema shaders (whatever they may be) to render their bitmaps. The bitmaps will be labeled for the frame to which they belong, when they are written into the /textures directory, next to the MXS file. So, the materials in each frame will reference bitmaps written specifically for that frame.
In case it helps, there is a kind of work-a-round where you animate the mapping coords for any given channel.
In this way you can animate a lot of things,.. probably using a b+w gradient map to control the roughness for example, then slide the (oversized) gradient left and right and the roughness will change at the spot where the map is passing through the geo.