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Currently, the `--cert <filename>` and `--overwrite` options for `pki-server subsystem-cert-update` command hasn't been implemented. This command automates the importing of the certificate passed as argument into NSS database and overwrites the existing one.  Also, necessary changes are made in the `CS.cfg` file.

Reference: http://pki.fedoraproject.org/wiki/System_Certificate_Renewal#PKI_10.4_or_later_2

Fixed in master:
* https://github.com/dogtagpki/pki/commit/d762073c4b5bcd4f9f30e3b8439983a497a77c97

I tested this on the PKI 10.5.1-5.el7 version.

I used following steps to verify this bug:

Upgrading subsystem certificate.

1. pki -d /opt/pki/certdb/ -c Secret123 -p 20080  ca-cert-request-submit --profile caManualRenewal --serial 0x4 --renewal

2. pki -d /opt/pki/certdb/ -c Secret123 -p 20080 -n "PKI CA Administrator for Example.Org" ca-cert-request-review --action approve <request_id>

3. pki -d /opt/pki/certdb/ -c Secret123 -p 20080 cert-show <cert_id> --output subsystem_cert.crt

4. pki-server subsystem-cert-update ca subsystem -i topology-02-CA --cert subsystem_cert.crt

5. certutil -L -d /var/lib/pki/topology-02-CA/alias/ -n "subsystemCert cert-topology-02-CA" # For verification of subsystem cert is updated in the database.

Restart the instance.

If the instance is started successfully then the certificate is updated successfully.

Verifying this bug.

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.

https://access.redhat.com/errata/RHBA-2018:0925