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Managed server always updates the entire configuration directory (DOMAIN_HOME/config/) in its local machine with the "config" directory from the admin server machine whenever managed server is restarted.
This is to ensure that managed server always gets the latest configuration whenever it starts. This is required and expected behavior.
I am not sure why you want to maintain a separate configuration for node2, all nodes in a domain always should have the same configuration (config.xml file).
May be if I understand your requirement, I can suggest a better solution to achieve it rather than trying to maintain a separate copy of configuration for node2 in config directory.
If you have any server specific files, you are encouraged to maintain them in DOMAIN_HOME/servers/<ServerName> directory. For example, domains/testdomain/servers/managedserver2/test/