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That is *definitely* where they end up, so, I'd double-check the book's sidecar folder for the metadata to see if they're actually in there (e.g., for foo.epub, check foo.sdr/metadata.epub.lua).
If they are, there's a bug somewhere.
If they aren't, they were never actually saved. Or the file was corrupted. Or emptied? (You mentioned KOHighlights, I don't remember if it might not offer some way of clearing them or something).
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