Linked input channels are automatically also linked in all flex mixes (aux, matrix, subgroup). But only if you link a flex mix and adjust panorama to full left and full right (by default set to center), you can hear a stereo signal in the flex mix. Also flex mixes are linked 1+2, 3+4, 5+6...
Flex mixes have three options: Pre1, Pre2 and Post(fade). I recommend to read the manual for details. If you want the flex mix follow your main mix, set the flex mix to postfade and the faders to the line on the scale. In analog times this was handled as "zero" (0 dB).