For logger errors:

su - zimbra
#find the regular and logger passwords
zmlocalconfig -s | grep mysql_password
#I didn't need to go any furthur because the logger processes stopped eventually and left it clean

this page had some info under "closed the table properly":
http://wiki.zimbra.com/wiki/Ajcody-Mysql-Topics

To archive all outgoing email:
1- Create an account with large quota. i.e: mailuser@domain.com
2- in /opt/zimbra/postfix/conf/main.cf add the line:
always_bcc = mailuser@domain.com
3- Restart zimbra
4- Login to mailuser acount and from options tab set a filter to discard all messages other than the specific user/s you want to audit.

To upgrade to a new version
-download version
-backup zimbra using snapshot and rsync
tar -zxf zcs...
cd zcs...
./install.sh --platform-override

-a hosts file error means that all the hostnames in /etc/hosts are not FQHN's

su - zimbra
zmcontrol stop
exit
become root
ps aux | grep zimbra (kill -9 pid# of any remaining processes)
mkdir /zcsbackuprsync
rsync -avHK /opt/zimbra/ /zcsbackuprsync/zimbra
mkdir /zcsbackuptars
tar -zcvf /zcsbackuptars/backup.zimbra.version.date.time.tar.gz -C /zcsbackup/zimbra .

My default Zimbra VM install uses LVM within its own virtual machine. This makes it harder to get at the data from outside the VM, and so complicates backup. The following steps need to be taken