That's something I never took time to fixe in the contrib itself. To remove the warning, you should create a custom template /etc/e-smith/templates-custom/etc/updatedb.conf/10conf (copy the default /etc/e-smith/templates/etc/updatedb.conf/10conf) and add the directory /var/lib/BackupPC to the PRUNEPATHS list, then expand-template /etc/updatedb.conf