After getting nothing more than a slap on the wrist in the form of a verbal and written warning, niantic has finally brought down some justice on cheaters and bots found in Pokemon GO. As of just recent, Niantic has begun putting a Slash Marking over any and every Pokemon that was caught or obtained illegitimately through a third party application. It has been said that these Slash Marking are given to any Pokemon that was obtain in a wrongful manner since April 15, 2017, but some might even go further back than that.
Slashed Pokemon WILL NOT be able to participate in the new gym System OR raid battles, they CANNOT be Evolved OR Powered-Up, and a player will receive ZERO Candy for them if they ultimately transfer these useless Pokemon. It is also expected that these Pokemon WILL NOT be able to be Traded to other players once Trading finally comes to Pokemon GO.