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I disagree with the previous commenter from 23 Nov, 2020.
This feature does not exist.
The following is from R12.0.1 FP1:
-> there is no delete option
If we open a server.id in the Admin Client, the option "Delete from ID File" is greyed out when we select e.g. a saml certificate.
So, there really is no option to delete obsolete certificates/keys.
This is already a feature. There is a built in tool you can use with the Domino server console.
Use certmgmt to view, import, export and delete certificates from the server's ID file.
certmgmt -? to view the help file which provides syntax.
If you'd like to use the GUI you can also copy the server's ID to the administrator's machine, and use the Admin client. Click Configuration > Certification > ID Properties. Browse to the server.id file that you copied, then click Your Identity > Your Certificates. Use the type switcher to change to Your Internet Certificates. Select/highlight the cert you want to delete from the list. Click Other actions > Delete from ID File.
At this point you can put the updated ID file on the server and restart Domino.