I don't know about the formats, but I don't think series info can be sent over unless you use Calibre to update the database on the device?
With that said, I'm not sure what Kobo would do when approached with this kind of complaint. The kepub.epub files are a product of conversion and not something that you're actually 'supposed to have', though the developers must be aware of the conversion plugin in Calibre. The 'cloud storage' for your kepub files is supposed to be the Kobo store.
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