You upgrade a single instance of NFO by installing the latest version over your existing installation. During the upgrade the installer package preserves all NFO configurations, except configuration files changed manually. These files, if changed, are backed up into conf-backup.<date>.tar.gz file (<date> is archive date), and should be restored manually, if necessary. The following is a list of some configuration files.
Default self-signed certificate
External Data Feeder for NFO certificate
Server configuration (Note: some Web GUI configurations are in this file as well)
Trusted certificates imported into Java Runtime cacerts keystore