In cloudmon, after making changes to the system name in agent.conf file, why this change was not discovered/updated in the Server?
Agent is already discovered by the controller. Controller configuration always overrides agent configuration.
Controller takes agent name (default Hostname, if name is not configured) during discover process. This agent is already discovered, so, if you want to do only from the agent.conf, configure name, stop agent and start agent after few minutes.
You can always override this name in Controller UI at the following location: settings > monitoring > agents > edit