As I said above, calibre will ONLY list content that is in the Kobo's database which is populated when the device is disconnected from a USB connection. You could try using NickleMenu to force a library scan on the Kobo
This database is NOT used by the koreader app on the Kobo.
As to how the plugin you mention koreader-calibre-sync locates content on the device I'll have to look at the plugin
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