I have literally just tried to add a custom ringtone, creating .m4r then adding it directly into /library/ringtones
Ringtone worked fine. Then 5 minutes later I have lost all native apps?? I have no settings/phone/messages/mail etc etc. have all games and 3rd party apps but literally nothing else? Sshing into device, I cannot even see any of the native apps there?
My only worry is that the ringtone was over 30 seconds long - I seriously cannot think of anything else??
Have you tried searching for them with the search bar on the farthest left page of the springboard?
I don't know if this will help but you'll be able to see if they have completely gone of if just the icons have gone