The AT32UC3L064 can be programmed through the UART-to-USB gateway. This can be accomplished using the UART boot loader preprogrammed in the device. Press and hold the mechanical switch while powering up the board to enter the bootloader, and use 32-bit AVR Studio to set up a programming connection to the device.
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If the default board controller firmware is replaced, programming of the AT32UC3L064 may not be possible as the UART-to-USB functionality might be missing.
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If any external programming tool is used on the AT32UC3L064, the boot loader might be erased, and it will not be possible to program the device through the UART-to-USB gateway. In this case the bootloader has to be restored with an external programming tool.