As with most all JR/Spektrum transmitters, the flap switch does not work by default. You will need to read the manual to make the flap switch work. See p68 of the DX6i manual (“FLAP”). Go to “ADJUST LIST”. Then scroll to find “FLAPS”. Use the scroll wheel to set the “NORM” value to up-100 and “LAND” to down-100. When you are done, the settings on your DX6i will look like the picture below. Now the flap switch will work. It will properly control the flaps in FS One rather than the flap position being otherwise neutral.
After making these changes, recalibrate your DX6i in FS One.