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Following the instructions in https://access.redhat.com/documentation/en-US/Red_Hat_Enterprise_Linux/6/html/Identity_Management_Guide/cas.html to renew an external CA certificate, the old cert was left in /etc/httpd/alias/cacert.asc . This subsequently lead to issues because ipa-replica-prepare uses that file.

Step 6 in the above guide should add the following command:
ln -sf /usr/share/ipa/html/ca.crt /etc/httpd/alias/cacert.asc

This is indeed a bug in the guide. The "Update the CA certificate in the file system" step in the "Install the new CA certificate on your first-installed IdM server", "Install the new CA certificate on other IdM servers with a CA" and "Install the new CA certificate on other IdM masters without a CA" chapters in the guide should be changed to:

  Update the CA certificate in the file system:

    # cp /root/ipa.crt /etc/ipa/ca.crt
    # cat /root/ipa.crt /root/external-ca.pem >/etc/httpd/alias/cacert.asc
    # cp /etc/httpd/alias/cacert.asc /usr/share/ipa/html/ca.crt

Changing the component to doc-Identity_Management_Guide.

I updated the commands in all three steps.