The more posts I see on these threads the more I realize how awful some of these reps are. Fear is just merely a tool fro them to stop people from having info. In this way, they make sure that people are scared enough and they will go back to them all the time to pay money.
Anyways, don't listen to them. The call center agents, CSE agents, ATI officers and immigration officers are different people for different tasks. Contacting CIC for the update does not have any impact (positive or negative) on your application.