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This bug is created as a clone of upstream ticket:
https://fedorahosted.org/freeipa/ticket/2918

Section ''2.6.1. Upgrading Packages'' states:
{{{
The update process automatically updates all schema and LDAP configuration,
Apache configuration, and other services configuration, and restarts all 
FreeIPA-associated services.
}}}

I think we should expand this information and add a note about ipa-ldap-updater:

{{{
Schema and LDAP configuration updates are done with /usr/sbin/ipa-ldap-updater
program. Unexpected LDAP upgrade failures may cause issues when using IPA. 
Thus, IPA LDAP upgrade log (/var/log/ipaupgrade-log) may be consulted for
errors happened during package upgrade.

When the cause of the failure is fixed, the IPA LDAP updater may be 
manually executed again:

# /usr/sbin/ipa-ldap-updater --upgrade
}}}

Fixed upstream
master: https://git.fedorahosted.org/cgit/freeipa-docs.git/commit/?id=989ba0aede11aac53d57ff1ea0e8df4edf4bace3

Verified the new note - 

The LDAP upgrade operation is logged in the upgrade log at /var/log/ipaupgrade-log. If any LDAP errors occur, then they are recorded in that log. Once any errors are resolved, the LDAP update process can be manually initiated by running the updater script:

[root@server ~]# ipa-ldap-updater --upgrade