I updated my atmega32u4 based boards with the Arduino Leonardo bootloader but unfortunately the Lufa projects I tried are not so happy with it. I have no clue why but I know it works fine with the original Bootloader so I reflased my boards with the previous CDC Bootloader. Having no AVR programmer in hand, I used one board that I fortunately did not update and flashed it with the Lufa AVRISP-MKII programmer. Here are some notes with steps and the needed files.
AVRISP-MKII
To build the AVRISP-MKII project, modify the following lines in the makefile:
MCU=atmega32u4
ARCH=AVR8
BOARD=ADAFRUITU4
F_CPU=16000000
Flash AVRISP-MKII on the survivor board
$ avrdude -p m32u4 -P /dev/ttyACM0 \
-c avr109 -U flash:w:AVRISP-MKII.hex
Bootloader CDC
Plug both boards together:
Flash the other boards with the Bootloader:
$ avrdude -p m32u4 -P usb -c avrispmkII \
-U flash:w:BootloaderCDC.hex
BootloaderCDC.hex can be found here
Make sure the fuses are correctly set up:
$ avrdude -p m32u4 -P usb -c avrispmkII \
-U lfuse:w:0xFC:m -U hfuse:w:0xD0:m \
-U efuse:w:0xC3:m