Problem solved.
Note the Serial Number of the revoked certificate in the JSS PKI. Then go into the MySQL database and run the following query to see if the is_revoked status is 1:
select * from certificate_authority_issued where serial_number='XXXXXXXXX';
If it is set to 1, we can reverse this to un-revoke the cert with this command:
update certificate_authority_issued set is_revoked=0 where serial_number='XXXXXXXXX';
