If during the setup for LsAgent, you've entered both a server address and a cloud relay key, LsAgent will always attempt to send the results to the server directly first, if this fails, it sends the results to the cloud relay.
The server listed in the .INI file is your local scan server you entered.
Settings in LsAgentConfiguration.xml are synced with your installation, but the file doesn't hold any connection info.
If you want to disable the direct server connection or the cloud relay connection, you can open LsAgent.ini and either remove anything after "Server=" or everything after "Agentkey="