IPhone – Notes disappeared from iPhone

I don't have a great answer - but this is fairly serious so I'm going to start an answer and hope someone else edits or answers if they can spot something I haven't.

On the computer, the only "red flag" would be if you wiped the phone of all content and settings, named it exactly the same name as it was before (which could be iPhone) and then backed up again and overwrote the backup with the actual data. iTunes tries hard to prevent this and spawn off a date-protected backup when it detects this, but I've seen this check fail and people lose backups from time to time. The remedy here is to restore the PC from a backup that has whatever MobileSync folder is the most recent.

On iCloud - you also shouldn't be able to overwrite a "full" backup with an empty one. Also, iCloud explicitly keeps several versions of the backups going back in roughly day intervals. It also normally stores backups for different devices without collisions or overwriting another backup.

The good news on iCloud is you can always get help from Apple at http://www.apple.com/support/icloud/ and from retail stores. New devices or ones covered by Apple Care also have phone or web support in most countries. All new Apple products have a 90 day window of set up help. Hopefully one of these can step in and assist. Not only does Apple get a data point where their tools let you down (and exactly what circumstances this happened) - they also see many people in this situation and will hopefully waste a minimum of your time getting this sorted.

Nevermind, I managed to get it working following the advise of another discussion thread on the Apple forums; namely:

Same thing happend to me on my 3gs, i went to Settings...iCloud...Delete Account then signed in again to add it. The iCloud inbox was displayed afterwards.

This also fixed the problem of notes, which now show up properly on the notes application.