"Making the change permanent" is a tricky concept. Every time you upgrade to a new release of Zimbra, all of those configuration files get overwritten, so you must be prepared to back up and restore them whenever you do an upgrade.
I don't like having to maintain multiple files, particularly since the upgrades may include new fixes that would be broken if I simply restored old files. For this reason I make all my changes in /opt/zimbra/conf/spamassassin/local.cf, which is a file that the releases don't change. That way I can simply back up and restore that one file and keep all of my custom tweaks. local.cf is the last file read by the system, so any settings in that file override equivalent settings in the other *.cf files.
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Cheers,
Dan
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