Just because they were transformed into candy confectionary people by the candy coven's magic, doesn't mean they can't stay in the junior agents group and go on missions.
Although the human agents couldn't understand what the candy kids were saying, or figure out who they were, or that they were even transformed agents at all, they did still recognise their usefulness. On this mission, the human agents they were sent out with, were captured and taken away. Fortunately these two went overlooked, as they froze stiff, pretending to be inanimate. On with the mission by themselves now, they find a poor marshmallow kid being experimented on and break him free. Me thinks if they ever see the other two agents again, they probably won't be human. But perhaps candy? Or some other animal.