Ok, I was able to find the correct path for the avrdude inside the arduino folders. I was also able to find the avrdude.conf file. And after a bit of work, I was able to create a command that avrdude would accept and seems to do something. My command looks like this:
avrdude -C avrdude.conf -c arduino -P com5 -b 19200 -p m16u2 -vvv -U flash:w:/16u2/16u2.hex:i
That works! I was able to flash the firmware to the 16u2. But, my Due still shows up as "USB device not recognized" in Windows. I guess it must be a further problem. Thanks all.