Stopping data collection or deactivating the agent will prevent or stop the FTR agent from collecting data or working but the script might be still running on your FTR host. If you want to stop your FTR script running, you need to stop the ftr.agent.service in your FTR host.
So if something bad happens in FTR monitoring and you want to "restart" all FTR stuff as a try, you could do the following.
1) in Agent status to stop the data collection for FTR agents
2) in Agent status to deactivate the FTR agents
3) in FTR host services to stop the ftr.agent.service
4) in FTR host to restart the fglam
5) you might need to activate the FTR agent and start data collection but you don't need manually start ftr.agent.service, which should be automatically started if everything goes right.