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This bug is created as a clone of upstream ticket:
https://fedorahosted.org/389/ticket/556

I had a custom certmap.conf as part of a pki-core install and after upgrading it was reverted to a standard certmap.conf.

389-ds-base-1.3.0.0-1.fc18.x86_64

This particular system had done some previous testing of these bits. When F-18 came out I wanted to sync it to reality so I did a: yum distro-sync

This downgraded to 389-ds-base-1.3.0-0.1.a1

Then I updated back to 1.3.0.0-1

Added a comment to "/etc/dirsrv/slapd-kvm-guest-02/certmap.conf" file and upgraded the instance from RHEL6.3 to RHEL6.4. The file's content is not updated after upgrade. Hence marking the bug as Verified.

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

http://rhn.redhat.com/errata/RHSA-2013-0503.html