I would recommend that you follow the steps below:
1. Disable notifications in Nagios XI for this server while you are upgrading the agent, so that your contacts wouldn't get flooded with notifications.
2. Make a backup of the "old" NSClient++ config (NSC.ini) just in case you have some custom commands defined. You are correct - the syntax is different, so you may not be able to use the same commands in most cases, but at least you will have a reference point.
3. Make a backup of your old scripts, located in the NSClient++ directory, especially if you have some custom scripts
4. Remove the old agent.
5. Install the new one.
6. Run the command for generating all of the "default" settings to the nsclient.ini file from the CMD prompt (as administrator). You will find the command somewhere in the top section of the nsclient.ini file.
Example:
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cd "c:Program Files\NSClient++"
nscp settings --generate --add-defaults --load-all
Note: You may see an error or two - don't worry about it. Open the nsclient.ini file to verify that it has been populated with all of the default settings (it should contain a lot more directives now, after running the above command).
7. Enable all of the modules under the [/modules] section, that you would like to use, save, exit and restart NSClient++ service, so that changes can take effect.
8. Test to see if you can monitor your system via NSClient++ and check_nt/check_nrpe, etc. (whatever you are using). You can run a couple of commands from the CLI on the Nagios XI server to check things out:
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/usr/local/nagios/libexec/check_nt -H <client ip> -p 12489 -s <'password'> -v CLIENTVERSION
/usr/local/nagios/libexec/check_nrpe -H <client ip>
9. If basic checks are working fine, then you can try adding any "custom" command that you might have, and testing them.
10. Finally, enable notifications in XI, provided everything works as expected.
Let us know if you run into some issues. Thank you!