O, never mind. Just solved the problem with tips from Programming Arduino Uno in pure C | Freedom Embedded
Just use the programmer id arduino and the correct device.
C:\Arduino\hardware\tools\avr\bin\avrdude -pm328p -carduino "-P\\.\COM6" -b115200 -F -Uflash:w:TestProject.hex:a "-CC:\Arduino\hardware\tools\avr\etc\avrdude.conf"