MonkeyBalls - thanks for the upvote. Yeah, updating it manually after adding graphics is very involved, and tedious to the point of being impractical. (EDIT: This is only the case when using separate sprites - if you're using self-draw mode, updating the scon file and the spritesheet image should update it) Once the sdk has the requested feature, I should be able to update the plugin to quickly support the reimport.
You should be able to update the runtime from C2 to C3 and things just continue working. Backup your project first, just in case, and let me know if you run into any issues.