I am a pilot and noticed when switching to iOS 5 all my stored charts, approach plates were along with all my books and aircraft manuals gone. I only use about 2.75 gigs out of 65 on my iPaD 1 so this is a lot more than just irritating and yes I can restore the books and manuals. This can be dangerous to the aircraft and pilots. Unintended consequences screwing with critical control systems can be more far reaching than may ever imagine. I do not use the iPAD for anything more than a check of where I am at, however I was considering installing ADS-B rcvr/tx and AHRS they work off Bluetooth or wireless network in the aircraft. ADS-B is a transponder type unit that lets approach know where you are and headed plus Receives near real time weather. I will probably not invest now since it is questionable if the data would be "cleaned" at the most inappropriate moment.
I would suggest apple discuss this internal decision to clean the memory of WingX charts and other aviation type software get invoved with the AOPA/EAA/GA by someone(s) from your company that is a pilot and has managerial authority to speak for them and understands that circling round a storm cell and this system dumps then you are likely to end up in a field somewhere dead or you have just passed your FAF and there is 500 ft ceiling. Finally hire a aviation controls engineer that can stand up in a meeting and say "this is stupid, you're going to kill someone and who did the safety analysis."