Okay, I figured out iCloud Notes syncing. Although it makes sense after using it, it's really not that intuitive IMHO. Here's how it works:
If you have all of your devices, iPad, iPhone and Mac Mail set to sync Notes with iCloud, all of your notes will appear on all of your devices. Great! If you turn off Notes syncing with iCloud on any one device, those notes will remain only on that device. Fine as well. However if new Notes show up in your Mail Inbox and you delete them, they will be deleted on ALL of your devices. The key is to not have them show up in your Inbox.
I hadn't noticed it, but a new "Notes" menu item appeared in my Mac Mail menu under "Reminders":
This is where all of the Notes are sync'd on your Mac. On iDevices they are in the Notes App.
The reason they would disappear is that the default in the iCloud Preferences is "Show notes in Inbox". So whenever I would create a new note it would show up in my Inbox. When I deleted it or moved it to another folder, it would remove it from all of the devices. To stop new Notes from showing up in my Inbox I had to make one change to my iCloud Account Preferences.
Here's how to access iCloud Preferences on the Mac
- Open Mail
- Control-click or right click on the Notes Folder or your iCloud account in the Mac Mail Inbox.
- Click on "Account Info" and the Account Info box will appear.
- Click on the "Mailbox Behaviors" tab and uncheck "Show Notes in Inbox".
That's it! Why the default is to have that checked instead of unchecked is beyond me. I unchecked it...I don't need new notes to appear in my Inbox and I don't want to delete Notes that show up there and wipe them from my iPad and iPhone either.
As I said, it's not very intuitive, but once I figured it out I find it works very well!
The same would go for deleting a Note from any one device as long as you have them set to sync with iCloud. If you delete a note from your iPad it will delete it from your iPhone and Mac...no matter where the note first originated.
Hope that makes sense and helps!