If you have a tool to unpack spritesheets, you can edit spritesheet.png and then unpack it again using the spritemap in sprites.json before converting it back to .c16.
https://github.com/Bazai/leshy_labs_spritesheet_cropper is a nice simple one if you are comfy with node! 
See this video for an example of spritesheet work:  https://www.youtube.com/watch?v=vLz0cjO8Pd8

Otherwise, you can just edit the sprites the old fashioned way.