It's not the best scenario for doing an upgrade but.... I'd suggest you do the following: block incoming mail at your firewall; disable Zimbra from starting at boot; use the NE backup to take a full backup of Zimbra; take a backup (using rsync, check the forums or wiki for details) of the /opt/zimbra directory structure; copy the backup off your current server; finally run the upgrade as you normally would for Ubuntu. When you've done the system upgrade see if Zimbra starts and runs OK, if it's OK the enable Zimbra to start at boot. You may also want to clone the server before the upgrade so you can do a restore if necessary.
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Regards
Bill
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