You have to 'convert' them to Mobi, after that all converted books have epub and mobi s available file formats. Nothing else changes within the library, so you won't even notice it, except that you library takes a bit more hard drive space than before.
Then connect the Kindle and send the books to the device.
If you send the books to the kindle before converting them, calibre asks you if you want to convert them before sending. That is an alternative way...
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