There is IMO no use for annotations other than on a PC (or similar) and per book. I use the "Kobo Utilities" in Calibre and it's fine.
If newly highlighted text & note isn't saved, then your database may be corrupt. Either restore a backup (made via Calibre or directly) or Factory Reset to rebuild the database. Then make sure you are on a recent Firmware. Some old versions have annotation bugs.
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Alas, at some point, something, somewhere went wrong and the process broke
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The "Annotations" plug in on Calibre fetches ALL the books. I don't have a use for that. The only reason it might not work is if the Kobo Forma database is corrupt.
The epubs and kepubs work slightly differently.