I think, and this is a theory, that the professor is grinding up Pokemon and turning them into candy to feed back to our Pokemon to make them stronger. Think about it, you can never get your Pokemon back once you transfer them and you get candy back that is specific to just that type of Pokemon. I think this is a cut and dried case of Soylentmon Candy. Okay may be not cut and dried, more like dehydrated and ground then re-constituted and caramelized with sugar and wrapped with a beautiful piece of paper?
It might be in an attempt to prevent Pokemon over population (they do seem to bread prolifically, I think Pidgies may take over the world soon.), or it could just be a sadistic twist of the professor. I’ve tried to communicate with several Pokemon I’ve sent and not been able to hear back. The professor has not been available to talk either, but he has been more than willing to take my Pokemon. This is all just a theory, but I think something is rotten in Kanto. I have been tempted to taste the Pokemon Candy, but I haven’t figured out how to get it out of the phone yet. Once I do I’m still not sure how to tell if it is made of the remains of another Pokemon, but I’ll keep investigating.
After posting this I was informed that someone else already had this idea and made a cartoon strip of it. I got this idea from a comment in a group chat, and I just ran with it, I had no knowledge of the pre-existing cartoon. Although I think the cartoon is awesome.