I just thought, this might be interesting to some.
We're running 4.5.10 Network Pro and trying to upgrade to 5.0.2 failed miserably.
First of all, the way, the server is a trial-server and the setup is a bit uncommon.
Main harddrive is /dev/hda3, the drive for opt and a few other bits is /dev/hdc1
/opt is symlinked to /media/hda3/opt
When i started the upgrade, Zimbra uninstalls the old components and starts installing the new ones, but even worse, it decides to remove the /opt symlink and installs the upgrade on /dev/hda3.
Suddenly the store and all configuration files are missing because of that behaviour.
My workaround for this was do a "mount -o bind" instead of a symlink, but really, Zimbra should not tamper with symlinks below /opt/zimbra, especially when there is other software installed in the /opt file structure.