It seems like Apple or Yahoo implemeted something on or around 17 May this year (that's the date after which my new or amended notes started disappearing) that didn't allow the sync between the iPhone Notes and Yahoo mail to function well, as explained in this Yahoo Messenger help topic, which was also coincidentally issued on 17 May 2013. It is however a problem that's been around on and off for a couple of years -
http://help.yahoo.com/kb/index?page=content&y=PROD_MAIL_CLASSIC&locale=en_GB&id= SLN5869
According to this, the problem lies with Apple's sync to Yahoo Mail as it creates a one-way sync AND deletes the original note from the iPhone. There is no return sync or 'copy all' mode to return the notes to the iPhone, so the only way to get the information back into Notes is by copying and pasting from Yahoo into a new note, time consuming and infuriating int his day and age. Also, you cannot do this from the iPhone mail app as the Yahoo Notes folder does not show up in this app!
The Yahoo solution is to copy the note contents into a new email (or I guess you could forward it), so that the email will show up in the sent folder in the email app.
An easier solution I picked up from an earlier message on this thread, is to move all the notes into a new Yahoo Mail folder you create, as that will show up in the email app. Still, you have to physically copy and paste each note...
I have tried all of the solutions suggested in this thread (I have an iPhone 4 using iOS 6.1.3) but I can't see how some have had success in getting notes back from Yahoo going by Yahoo's explanation. My only guess is that they also had iCloud or Gmail set up to receive notes as well and these are the ones showing up in Notes, not the ones copied to Yahoo. People saying "some turned up, others didn't" or "you end up with a few duplicates" seem to indicate this is the answer. Another solution mentioned said to select the ‘Notes’ switch to ‘on’ in all of the mail accounts under the ‘mail, contacts, calendars’ settings. This means that the note is backed up to Yahoo Mail (and all the other accounts selected) and remains on the iPhone, but simply because the other email accounts do not delete the note when backed up.
So my suggested solution is this -
Go to your Yahoo mail account on your computer or via Yahoo Mail app/Safari on the iPhone, NOT via the email app.
Go to the Notes folder, select all notes (you have to do this for each page of notes) and select move and select ‘new folder’ under the drop down menu (or create a new folder before doing the move). All your notes will be safe in this new folder and will show up in the iPhone email app under your Yahoo account.
Go to the iPhone ‘mail, contacts, calendars’ settings, deselect the Yahoo account for Notes back up. Either select iCloud, Gmail or iPhone only (except this will not make any back up of your notes which will be lost if you lose your phone). This will prevent your newly reconstituted notes from syncing to Yahoo Mail and being deleted from the iPhone.
Then open each note in turn, select all, copy, go to Notes open new note and paste. Close.
After a test the notes remained on the iPhone (presumably because they are syncing back and forwards with iCloud and Gmail) but oddly though, even after doing this a test note I made and synced to Yahoo only still remains on the iPhone… ***!!!
The most annoying thing about this is the fact that the problem has been around for at least 3 years on older iPhones and iOS versions, yet Apple don’t seem to have said anything on the subject or tried to figure it out. Seems like Apple’s reliability is going the way of Windoze.
I also object to the fact that the only reliable solution is iCloud. I have no wish to trust all of my information to the cloud and no wish to buy additional storage once the free allowance fills up. Makes me wonder if this is what is driving Apple's apparent lack of interest in resolving this problem.
Still trying to find a guaranteed solotion.