I have tried my luck around with all the helpers: `pki-server cert-fix`, 
`ipa-cacert-manage`, `ipa-certupdate`, etc. but each one is failing on me for 
multiple reasons.
- `ipa-cacert-manage` Cannot update the CA with `--external-cert-file` because 
the root ca is not detected to be in the trust list
- `ipa-cert-fix` Was run without overlapping validity time, and the certificate 
were re-created, so now it is not recoverable, neither back in time, nor in 
current time
- `pki-tomcat` is failing

It is quite a mess and I would like to ask for some guidance on how one could 
recover manually from  such dependency issues:
- Is it possible to do a `ipa-server-install` and keep the user data?
- If I sign all of the service's certificates manually, what are all of the 
manual steps needed to get the services back up so that the helpers can be run.
  - I've tried to install the CA certificate in the nssdb database, ldap, and 
/etc/ipa/ca.crt. Are there other locations?
  - I've recreated an httpd certificate signed by the root, but I can't figure 
how to do the same with the ones located in the nssdb database, i.e. to 
recreate a csr with the same data as one of the certificates there
- What is the order of services that should be updated. My understanding is CA 
-> `certutil`'s CA -> httpd + slapd + pki-tomcat (not sure where the last one 
is or how to edit it) -> `ipa-certupdate`
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