The above programmers communicate with the bootloader program on the device. The bootloader is a small program located at the end of flash which has the sole purpose of loading a new program. To tell the device to go to the bootloader, hold button 1 down at powerup. Alternately, if the device is configured for usb-cdc mode, or uart mode, then send the escape character '\033' to the device. In rare circumstances (if you load bad code AND the device has the default bootloader) you will need to open up the device; to force the bootloader in hardware: power it on, then short the two bootloader pins (force bootloader at reset), then short pins 1 and 5 of CONN2 (reset the device) Now the device should be in the bootloader.
There are two files, one ending in .hex, the other .eeprom.hex. The .hex file is the main software program and resides in flash. The .eeprom.hex file goes in eeprom (memory on the device which is easier than flash to read and write, and isn't erased at loss of power) which mainly stores settings and default parameters. You must program both files for the device to work correctly.
If you are using the dfu-programmer, you can program the device with:
dfu-programmer at90usb1287 erase dfu-programmer at90usb1287 flash-eeprom surveydevice.eeprom.hex dfu-programmer at90usb1287 flash surveydevice.hex dfu-programmer at90usb1287 startReplace surveydevice with the correct filename.