"Each end-user app can be used as a collection tool by the app creator, invisibly collecting and forwarding data to the app creator without the knowledge of the end user," Niantic writes. "These apps can have an effect similar to DDoS attacks on our servers."
The company says it's rearranged of few things in its back-end and can reverse bans on a "small subset" of accounts. That won't apply to accounts doing nothing but remotely accessing and capturing Pokemon, taking part in gym battles or grabbing supplies from Pokéstops. In fact, it sounds like bans for those terms-of-service-violating activities will become even more strict.
"Our main priority is to provide a fair, fun and legitimate experience for all players, so, aggressive banning will continue to occur for players who engage in these kinds of activities."