Have you read this?
"3.4 Programming the ATxmega128B1 through the USB interface
The ATxmega128B1 can be programmed through the USB interface. This can be accomplished using the USB boot loader that is preprogrammed in the device. The boot loader is evoked by shorting pin 6 on J1 to GND before applying power to the board. A 100mil jumper can be used. Programming is performed through the FLIP plug-in in AVR Studio (which can also be started as a standalone application). NOTE If any external programming tool is used on the ATxmega128B1, the boot loader might be erased, and it will not be possible to program the device through the USB interface. In this case, the boot loader has to be restored (available on the Atmel website) with an external programming tool."
"3.1 Downloading the firmware
If the on-chip Atmel ATxmega128B1 firmware needs to be downloaded into the XMEGA-B1 Xplained kit, this could be achieved by using one of the following methods:
• Using the ATxmega128B1 on-chip DFU bootloader and FLIP (please refer to Atmel AVR1619 application note about using the on-chip DFU bootloader with ATxmega128B1)
• Using the Atmel AVR Studio® 5 and the regular Atmel AVR tools like JTAGICE3, AVR ONE!, or JTAGICE mkII (please refer to the on-line help of AVR Studio 5 about how to use it for part programming)"
AVRDUDE is not mentioned in either document.
I don't see Atmega128B1 listed in avrdude.conf (in IDE 1.8.2, the latest I have), I would think support there would be a prerequisite, yes?