Hi jd1000,
If you need to reset the device to factory settings I would recommend you to erase the image of the board on the SD card and install it again using the latest firmware available. You can download it again from here https://communities.intel.com/docs/DOC-22226 . The firmware can be upgraded in the Galileo IDE.
If you only need to change the value of some of the gpio take a look at http://www.malinov.com/Home/sergey-s-blog/intelgalileo-configuringtheserialportinlinux .
Regards
Sergio