Hello,
Today at least some options (related to the activation or not of some markup extensions, the activation of the plugins, the synchronization target...) are not backed up. And hence lost if one relies on such a backup.
At the same time Apple documentation for users claims that iCloud backups create a copy of information on your iPhone that is not already synchronized with iCloud, which means that basically you should not loose anything after a backup and a restore !
So the idea here would be to include all the settings (excluding passwords maybe ?) in iCloud backups scope so as to be able to retrieve them after restoring an iCloud backup, which in particular would allow to launch a sync straight away to get back one's notes !
Thanks !
Regards,
Grégory