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I often move between the Kobo iOS apps and my Kobo Clara. To ensure a sync, I will exit out of the book in either the app or reader. This forces a sync to the cloud. Otherwise, the sync happens at a more leisurely pace—usually long after you've found your last location manually!
I regret to inform you that page location is generally all that syncs between iOS apps and the reader. I find bookmarks, highlights, and notes sync might sync once when the book is first opened in the iOS app, then never again. It's as if they are on two different databases. I haven't found a solution for it yet. I'd rather annotate on my iOS device. It's so much easier. Kindle has one over on Kobo on this particular feature. It's a shame.
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