According to CloneCD web site, your writer shouldn't be able to make backups of SD2 protected games, 'cause of missing capability of "correct EFM encoding of regular bit patterns"; btw, the last cloneCD version (3.2.1.1) has an option (Amplify weak sectors) that enable writers to write better sectors generated by a burner that hasn't the EFM encoding capability. As usual, try and make me know if it works....personal experiences are always the best answers we can achieve .

Hope that this can help