atmel ice or avr dragon i guess are the normal ways to flash the chip from atmel studio, I posted some options for flashing the firmware here https://forum.duet3d.com/post/147110 based on stuff that many of us may have lying around.
the other thread you posted to say the 3x3mm vqnf chip is the -mm part number, if your chip is 4x4mm qnf use the -mu (or -mf) part number?
(edit -mf was the 125C industrial temp range, -mu the 85C consumer range)
