After some research, I tracked down what seems to be the most recent copy of the zip file (20831 bytes) for Atmel Application Note AT09002 which was stored in the Wayback Machine (archive.org) on 1st August 2017:
Atmel-42305-SAM-I2C-SPI-Bootloader_ApplicationNote_AT09002.zip
It contains the Python tool hex2fy.py and config files which you mentioned.