Notes missing after upgrade to iOS 10

If you didn't backup the notes with iTunes or iCloud, then they are gonna permanently. On iPhone, there are two different kinds of notes: one is synced with iCloud and the other is local notes. I am aware of this after switching to a new iPhone. I guess the missing notes were stored locally.

Make sure that you visit www.icloud.com and verify that your notes are present there. If it isnt there then its likely that you have notes being saved to an email that you either currently have, or used to have.

If neither is present, check iCloud settings on your iPhone for iCloud backups and check iTunes for iOS backups and see if you have a backup that existed before you updated. If you have one, then you can restore it and then try to see if the notes come back.