LTC4162-SAD Demo Circuit 2038A Programming problem


I tried to use the Arduino/Linduino code from the LTC4162 SDK to change the code running on the Atmel device found on the 2038A demo circuit to run my own custom application.I am trying to debug my way through this at present without much luck. 

[Please NOTE:In the SDK readme there is a line that states "This project is compatible with our Linduino development platform ( The file location  listed semms to point at a broken link - page not found Error]

Whilst trying to get my own application code running in Arduino I came to a point when nothing  was compiling so I thought I would go back to the origional application that runs with the GUI. When I start up the GUI I tried to use the "program Default Firmware button".... but after a few minutes I get an error stating that "GenuinoZero Bootloader NOT found. Programming Failed!"

Have I now got a bricked demo board? - any suggestions on how to get back to the out of the box experience??