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I had the same - finally straightened out. It was Kobo, not Calibre.
I normally download to the computer and stick the files on the SD card. Put the card into Kobo Glo, and it reimported quite a few of them if the date and author were different. (some books show "unknown")
I've always transferred that way - I might be using an Android tablet (which uses a card) a Windows laptop, and a Mint desktop which may see or not see the device.
Easier to bring the card to the reader since all of them see the card.
I won't use cloud storage. There is a need for some hard and fast rules if a company changes its mind about "free" (windows just did) or any other policy.
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