The root cause of the problem was Selinux... it detected that I changed the cert and was preventing it from being read as malicious?
So I had to issue following command for it to accept it.
# restorecon -RvF /etc/pki/tls/private/jira.key
restorecon reset /etc/pki/tls/private/jira.key context unconfined_u:object_r:user_tmp_t:s0->system_u:object_r:cert_t:s0
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