So the OS when it does a once a year-ish major upgrade might delete some of the data. This would be realised by any prudent pilot 1. after the upgrade and if that didn't work 2. before getting in the aircraft, or 3 before engine start when one can't find the chart to brief the departure.
The only way this "iPad can delete charts" sky-is falling-pilots-will-crash headline is going to occur is if you upgrade to iOS5 in flight. Hardly a likely scenario.
This is along the lines of antenna-gate. Yes, you can cause it to be a problem if you try, but use it normally with the usual prudence and it's a great device.
And as for our Huxley lover with the scaremongering that: "iPad unauthorised as it blanks PFDs and Boeing's issuing a SB": Read your link it's talking about leaving the iPad connected to the 3G etc network to get live info. That's a world away from "Airplane Mode" using one's Jepp charts etc.
Bottom line is that if your regulator and company allow it and have done an appropriate risk analysis on the device, implemented mitigators and have sops for its use, go for it.