How can I recover notes missing from the Notes app?
This is a little like what happened to me, I posted a question here relating to notes that had gone missing too. 

It seems that if you take a note while offline, when you sync with icloud it will sometimes without warning delete notes it does not know about :( Luckily in my case since I had made the note on my mac it created a recovery folder for me. 

Perhaps your phone may have done a similar thing? If you open notes and hit the 'accounts' button at the top, is there a 'recovered items' folder?