You may receive the "Error (209014): CONF_DONE pin failed to go high in device 1" error when you are trying to configure your device via JTAG using a .sof file and you have incorrecly set the device in your Quartus® II project.
For example, if you have your Quartus II project set for an Engineering Sample (ES) device and compiled the design and used the generated .sof file to program your board that has a production device. This also will apply in the reverse where your board contains an ES device and your design was targeted for a production device.