We were running zcs 4.5.10 on CentOS 5 for one year with no problems. During that time we have migrated the system two times (from one server to another with the same setup). The last time the migration happened, ALL users lost their email for the previous two months. The migration was done by rsync of the /opt/zimbra folder, updating dns/hosts/firewall and so on.
It turns out that the missing email is in the email store /opt/zimbra/store.
Re-indexing the mailbox has no effect.
The mail is there but zimbra won't show it. We've upgraded to the latest version of zcs and updated our server. No luck.