Only relevant for holdouts like me, but El Cap Notes don’t reliably sync with iCloud. They seem too, but I think there are issues with rich text notes and shared notes (of course you can’t see which are shared or unshared in El Cap). There’s also something odd with sync of those that do work, I had to toggle Notes on/off in iCloud to force a sync update.

If you’re on El Cap you need to use iCloud Notes via a browser.