Two Weeks ago, i've tried to make this upgrade , but it's fails.... That's what i made;

In my Zimbra Store server (Zimbra version 3.1.3)

1.- Shut Down Zimbra Services
2.- Backup /opt/zimbra, /mailbox (here is store, db, log, logger)
3.- Run 4.0.2 installer and got this error message:

Code:
Checking for installable packages

Found zimbra-core
Found zimbra-ldap
Found zimbra-logger
Found zimbra-mta
Found zimbra-snmp
Found zimbra-store
Found zimbra-apache
Found zimbra-spell


The Zimbra Collaboration Suite appears already to be installed.
It can be upgraded with no effect on existing accounts,
or the current installation can be completely removed prior
to installation for a clean install.

Do you wish to upgrade? [Y] Y

Select the packages to install
    Upgrading zimbra-core
    Upgrading zimbra-ldap
    Upgrading zimbra-logger

Install zimbra-mta [Y] N
    Upgrading zimbra-snmp
    Upgrading zimbra-store
    Upgrading zimbra-apache
    Upgrading zimbra-spell

Installing:
    zimbra-core
    zimbra-ldap
    zimbra-logger
    zimbra-snmp
    zimbra-store
    zimbra-apache
    zimbra-spell

The system will be modified.  Continue? [N] Y

Shutting down zimbra mail

Backing up ldap


Removing existing packages

   zimbra-ldap...done
   zimbra-logger...done
   zimbra-snmp...done
   zimbra-store...done
   zimbra-spell...done
   zimbra-apache...done
   zimbra-core...done

Removing deployed webapp directories
Installing packages

  zimbra-core......zimbra-core-4.0.2_GA_362.RHEL4-20060924201056.i386.rpm...done
    zimbra-ldap......zimbra-ldap-4.0.2_GA_362.RHEL4-20060924201056.i386.rpm...done
    zimbra-logger......zimbra-logger-4.0.2_GA_362.RHEL4-20060924201056.i386.rpm...done
    zimbra-snmp......zimbra-snmp-4.0.2_GA_362.RHEL4-20060924201056.i386.rpm...done
    zimbra-store......zimbra-store-4.0.2_GA_362.RHEL4-20060924201056.i386.rpm...done
    zimbra-apache......zimbra-apache-4.0.2_GA_362.RHEL4-20060924201056.i386.rpm...done
    zimbra-spell......zimbra-spell-4.0.2_GA_362.RHEL4-20060924201056.i386.rpm...done

Setting defaults from saved config in /opt/zimbra/.saveconfig/config.save
   HOSTNAME=canelo.midomimio.cl
   LDAPHOST=
   LDAPPORT=
   SNMPTRAPHOST=canelo.midomimio.cl
   SMTPSOURCE=admin@midomimio.cl
   SMTPDEST=admin@midomimio.cl
   SNMPNOTIFY=yes
   SMTPNOTIFY=yes
   LDAPROOTPW=ZZZZZZ
   LDAPZIMBRAPW=ZZZZZ
Restoring existing configuration file from /opt/zimbra/.saveconfig/config.save...done
chown: no se puede acceder a «/opt/zimbra/conf/smtpd.key»: No existe el fichero o el directorio
chown: no se puede acceder a «/opt/zimbra/conf/smtpd.crt»: No existe el fichero o el directorio
Operations logged to /tmp/zmsetup.log.23794
Setting defaults...Setting defaults from existing config...Done
Upgrading from 3.1.3_GA_474 to 4.0.2_GA_362
Sat May 12 14:25:45 2007: Stopping zimbra services
Sat May 12 14:25:50 2007: Starting mysql
UPGRADE FAILED - exiting
After that i've tried to start the server but it does not start:

Code:
[root@canelo zcs]# su - zimbra
[zimbra@canelo ~]$ zmcontrol status
Cannot determine services - exiting
[zimbra@canelo ~]$ zmcontrol start 
Host canelo.conaf.cl
        Starting ldap...Done.
        Starting logger...Done.
        Starting mailbox...Done.
        Starting snmp...Done.
        Starting spell...Done.
[zimbra@canelo ~]$ zmcontrol status 
Host canelo.conaf.cl
        ldap                    Running
        logger                  Stopped
                logmysql.server is not running
                zmlogswatchctl is not running
        mailbox                 Stopped
                mysql.server is not running
        snmp                    Running
        spell                   Running
After Hours triying to fix this, i downloaded the backup and i got the same errors, so , i have rebuild the logger mysql db and add the following line in sudo config (visudo), because, when i run zmcontrol start, its promt for a password:

root ALL=(ALL) ALL