After deleting a template in ChangeAuditor it is still in affect on the servers with agents installed.
If it has been less than 15 minutes, the agents may not have the new configuration. The polling interval for agents refreshing their config is 15 minutes by default.
Wait for 15 minutes and make sure the templates in question are no longer active.
You can refresh the configuration of any agents that the protection template was assigned to or alternatively, you can also restart the ChangeAuditor Coordinator service to force the agents to reconnect and download the new configuration.