Do you mean you have transferred the books from Calibre onto your Kindle, and although they show up as being on your Kindle when you are viewing them via Calibre library, they aren't appearing on the Kindle itself?
If so, on your Kindle have you made sure to change the sort options from "All" to "Downloaded" because Amazon recently changed this and "All" means all the books in your Amazon cloud, while "Downloaded" means all the items downloaded to your device (and that can mean books not bought from Amazon and sideloaded from your computer to your Kindle. Previously it was "Cloud" and "On Device", which makes more sense.
So set the options in the home screen of your Kindle to "Downloaded" and possibly also "All items" or "Docs" too if they don't show up.
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