Hi,

I would start by doing a backup of the NSS database (save the directory and 
files from /etc/pki/pki-tomcat/alias).
Then remove the wrong cert using:
certutil -D -d /etc/pki/pki-tomcat/alias/ -n 'caSigningCert cert-pki-ca'

and install the good one using
certutil -A -d /etc/pki/pki-tomcat/alias/ -n 'caSigningCert cert-pki-ca' -I 
/etc/ipa/ca.crt -t Ct,C,C

and try to restart the whole stack with ipactl restart.

I’m not sure this will work, it really depends whether the original key is 
still in the nss database. There may also be other places where the CA cert has 
to be replaced.
flo
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