In Quartus II version 12.0, if a valid configuration is not selected in the Nios II Application Property Page, the settings set in the Nios II Application Property Page cannot be saved.
Also, if you edit the Nios II application properties, you may lose a valid configuration.

Before editing settings, manually select a valid configuration in the Nios II Application Properties page.

For details, please refer to the URL link below.
  https://www.altera.com/support/support-resources/knowledge-base/solutions/fb31565.html