There were three tricks to get our 32-bit --> 64-bit upgrade to work
a) The instructions here
https://fedoraproject.org/wiki/Upgra...a_5.0.13_64bit were the most helpful, easiest to follow and shortest. For example, on the fresh, new install, there's no reason to worry about all the detailed installation settings since you can copy them from the 32-bit version. The settings are mostly in $ZIMBRA_HOME/conf/* The only items that we ensured where identical were 1) hostname, 2) default zimbra domain. The IP was not and we have multiple zimbra domains and removed many of the default accounts. Anything stored inside LDAP wasn't important to match.
b) If you've extended your LDAP to support POSIX and/or SAMBA, don't forget to pull the nis.schema and samba.schema files over from the original install.
c) Don't try to mix versions. Go from 32-bit X.Y.Z to 64-bit X.Y.Z All data is completely compatible **except** the LDAP data stores, IME. This is clearly stated everywhere that I've read.
The 5th upgrade attempt took less than 30 minutes from start to finish. 20 min of that was rsync'ing data from the running system (no downtime), then we brought the running system down and re-did the rsync cmds again to get "clean" database files. The first 4 attempts were following the official instructions, but we were unable to get them working. We don't know why.
Our 32-64-bit migration was for 5.0.9 CE on Ubuntu Server 8.04.2 LTS running under 64-bit Xen.
The "officially" provided instructions
Network Edition: Moving from 32-bit to 64-bit Server - Zimbra :: Wiki are not as easy to follow as those referenced above. I can understand that most deployments will want to follow those. Perhaps our configuration with Posix, Samba and multiple domains is part of the issue for our upgrade.