Use SceneReader to unpack Battle/Scene.bin into individual chunks.
Then use the Hex Editor to translate it... it's time consuming but I don't think there is an easier way. (Could be a tool out there!)
Make sure you dont inflate the files, if you add bytes, clip the same amount you added off the end of the file (make sure you only clip padding).
Once it's done, SceneReader can rebuild your Scene.bin. Hurrah!