Solved!
I SSH'ed into root, then cd'd to usr/bin/ and then "vi run-avrdude"
This brings up the text editor and the line that says
"elif [ $profile == 'mega2650' ]; then
avr -c linxgpio -C /etc/avrdude.conf -p m2560 -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m"
change the "D9" to "D0" and it worked! EEPROM is saved after uploading a new sketch.
the text editor VI is tricky to learn but I figured it out.