We have an iPhone app with several thousand users, and we've had one or two users saying that after a full backup & restore procedure within iTunes, the data for our app was lost.
All the data (photos & SQLite DB) are stored in the documents area of the app. I've tested this thoroughly with our devices and it works absolutely fine.
Can anyone think of a reason for this, or has anyone experienced this before?
I have this problem too - sometimes iTunes goes berserk and deletes data. Most apps are not important enough for people to complain, but if yours is you will hear about it. As it seems, you do.
My theory is that something goes wrong in iTunes and it uninstalls the app deleting the data, and then reinstalls it back - fresh and minty.
One thing I can suggest is storing data in both Keychain and Documents folder, and looking in both of these places. When an app is uninstalled the keychain is NOT cleaned up, at least not right away. However when backup is restored to a different device keychain is not carried along, so Documents is still a must.
The other option is to encourage online backup with user's permission. Of course you need to control access so that's a bit of a bother.