servermgrd certificate in Yosemite server chain of trust
servermgrd looks up the certificate it uses for port 311 via an identity preference named "com.apple.servermgrd". By default, the preference points to the self-signed "com.apple.servermgrd" identity cert. After you change the preference you can remove the old self-signed cert without causing any harm. But you must make sure that the access control list (ACL) on the private key of the certificate that you want servermgrd to use allows servermgrd access. 

If servermgrd cannot access the private key, it will delete the preference and create a new self-signed identity and set a new preference to point to the newly created identity cert.