I initially configured my xcodeserver to use a certificate of mine.
Then I "Allowed Xcode server to manage my certificates and profiles", and revoked the previous certificate.
It worked for some time, but now it often tries to use my certificate and fails because that certificate has been revoked.
I did find that, in the bot configuration sheet, then "Signing", then "Certificate and profiles", it's possible to right-click on a certificate, but the "Remove from server" that appears then is greyed and disabled.