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The books already on the ereader have a green tick in the row. So you'd only send ones not on the device.
It wouldn't usually create a duplicate, but overwrite if you did resend.
You can also in Calibre view what is on the ereader and add to the library, though that only works for DRM free ebooks.
In general, for any app or ereader, never load direct from a shop online to the ereader or app, but "download to PC" (inc Mac, Linux, Windows etc) and import to Calibre. Having plugins to remove DRM for bought ebooks is needed.
You don't own Library books (includes Kobo Plus and Amazon Kindle Unlimited as those are subscription libraries) so you shouldn't remove DRM from them. Some only work direct on an ereader or direct to an app, or sometimes via ADE to a registered eReader or app.
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