A customer ran into this yesterday, and here was the workaround; hopefully this will work for you.
The Workaround
-----------------------
1) zmcontrol stop
2) Do the steps as outlined here:
Optimizing 50 to 60 LDAP upgrade - Zimbra :: Wiki
3) Do the steps as outlined here:
Installing custom ldap schema 6.0 - Zimbra :: Wiki
4) cd /opt/zimbra/data/ldap **rename all ldap.* files so they are out of the way**
5) Copy the latest ldap.bak from latest backup (most likely from 5.0.x), and place it in /opt/zimbra/data/ldap/
6) chown zimbra:zimbra /opt/zimbra/data/ldap/ldap.bak && chmod 640 /opt/zimbra/data/ldap/ldap.bak
7) mv /opt/zimbra/data/ldap/hdb /opt/zimbra/data/ldap/hdb.OLD
8) mkdir /opt/zimbra/data/ldap/hdb/db && mkdir /opt/zimbra/data/ldap/hdb/logs
9) chown -R zimbra:zimbra /opt/zimbra/data/ldap/hdb/
10) Edit the .install_history file, so it will the install section, for example:
1252187141: INSTALL SESSION START
1252187141: UPGRADED zimbra-spell-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187142: UPGRADED zimbra-logger-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187143: UPGRADED zimbra-ldap-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187144: UPGRADED zimbra-archiving-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187145: UPGRADED zimbra-core-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187146: UPGRADED zimbra-snmp-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187147: UPGRADED zimbra-convertd-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187148: UPGRADED zimbra-mta-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187149: UPGRADED zimbra-apache-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187151: UPGRADED zimbra-store-6.0.0_GA_1802.RHEL5_64-20090830130556
1252187143: INSTALL SESSION COMPLETE
**You only need to delete the CONFIGURED/UPGRADED for 6.0.x section, keep the 6.0.0 INSTALL session. Make sure to keep *everything* that every came before...every 5.0.x install, etc**
11) Run /opt/zimbra/libexec/zmsetup.pl