Well, once it happenned to me:
I am from Spain, so in my Logbook that is my country. I set up a mission as usual, with Red Alliance containig only Russia, and every other country (included Spain) belonging to Blue Alliance. Then I created a flight group and selected the group's country as Russia (Red). Afterward I created a enemy ground group (Blue), and selected Spain for its nacionality.
Fired up the mission and killed al the enemy units, as usual :D, and when I exited from the mission I was informed I had commited "Fratricide" and all my combat points were erased... so they were set to zero.
So if you are, let us say an USA citizen and your Logbook reflects it, you better do not kill USA units ;), even if you fly as a russian pilot and USA is in the enemy alliance.
Maybe I am mistaken, so any input on this subject is welcome.