Abbreviated mostly from: https://docs.microsoft.com/en-us/troubleshoot/windows-server/windows-security/decommission-enterprise-certification-authority-and-remove-objects
Several notes:
These instructions assume that all issued certificates are expired. If the issued certificates still exist and are active within the expire time or are revoked, you will need to go through a set of steps to revoke the remaining issued certificates and update/transfer the revocation list to the current PKI systems. Generally you can just remove the certificate templates from the old server and let the certificates expire or be re-issued by the newer issuing servers. It all depends on how quickly the old PKI server needs to be removed from inventory. Steps are different on a single-tier PKI set up, so don't do this unless you are sure!
Get and pair the server name and CA name. This will show all info about all CA servers, so choose the server name wisely. From PowerShell or CMD terminal as admin:
certutil
Shutdown certificate services on the server being decommissioned:
certutil -shutdown
Delete CA private key using the name gathered from above (I have had issues with this step and probably is not important if you securely erase the drive immediately after server decommissioning):
certutil -delkey <"ca name">
Uninstall Certificate Services:
"Server Manager", "Manage", "Remove Roles and Features" Click through wizard and de-select "Active Directory Certificate Services"
Restart the server.
ONLY do the following if issued objects like CRL and AIA no longer matter! DO NOT remove the Certificate Templates if you are replacing this PKI server!
Remove CA Objects from AD:
"Server Manager", "Tools", "Active Directory Sites and Services" Select appropriate icon in left window pane, "View", "Show Services Node" "Services", "Public Key Services" Under the "AIA", "CDP", "Certification Authorities", and "Enrollment Services": Delete the CA object NOTE: should already be missing under "Enrollment Services" because it is removed during the removal of certificate services.
There are more advanced cleanup procedures in the link at the top if you feel that these deletion steps did not work properly.
There is also a method to recover the certificate templates if they are deleted.