The syntax is:
UnitName SetFlagTexture "Texture"
Where unitname is the name of the flag, and texture the flag er... flag.
Valid textures are (for OFP v1.46):
usa_vlajka.pac
west_vlajka.pac
rus_vlajka.pac
First is for the American flag, second for the NATO flag (I never managed to get this one to work) and the third for the Russian flag. Hope it helps