Ok, after a bit more digging I have discovered the FlightPlan folder in iOS is in a hidden folder (.Contents) within the main FreeFlight6 folder. I thought it was a bit strange because when you view the FreeFlight6 folder it states there are 4 items within (on my particular install). However, when you open the folder, only 3 items are visible. The .Contents folder holding FlightPlan is invisible.
So, the only way of getting to the FlightPlan folder is to do a search in files, which then brings it up.
Hope this helps anyone else looking for FlightPlan in iOS.