I configured my Kindle Fire HD to only support AZW3 in calibre, so all my books, even MOBI files are converted. I was having issues with MOBI files someones not showing up under my Library.
Currently, the only books showing up under Docs are PDFs.
Do you have a file explorer on your Kindle Fire? I downloaded Es File Explorer and found that a Calibre copies books to /sdcard/Documents/. Maybe you should make sure that Caliber is coping the files to that location
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