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At moment to remove SSL certificate you need to manually remove folder containing certificate from /var/aegir/config/ssl.d/ and /var/aegir/config/server_master/ssl.d/ if exists. In addition to this steps you need to delete the entry for the certificate you are deleting in the hosting_ssl_cert MySQL table.
So it would be grate if there was an interface to do this steps. It would be more grate if there was an interface to do add certificates.