Nie wiem jak w przypadku wybranego przez Ciebie bootloadera, ale z fabrycznym DFU musisz zrobić:
"2.5.1 Programming with USB bootloader: DFU (Device Firmware Upgrade)
AT90USB part comes with a default factory pre-programmed USB bootloader located in
the on-chip boot section of the AT90USB. This is the easiest and fastest way to
reprogram the device directly over the USB interface. The “Flip” PC side application, is
available from the Atmel website, offers a flexible an user friendly interface to reprogram
the application over the USB bus.
The HWB pin of the AT90USB allows to force the bootloader section execution after
reset. (Refer to AT90USB datasheet section “boot loader support”). To force bootloader
execution, operate as follow:
Press both “RST” and “HWB” push buttons
First release the “RST” push button
Release the “HWB” push button"