Frankly I have no idea how you managed to empty your Kindle.
To get the books back, go to the Content and Devices page on Amazon. Select a book, choose "Download and transfer via USB" from the drop-down menu and your Kindle as a target. This downloads the book file to your computer. Don't try to open it. Connect the Kindle to the computer, drag and drop the file to the documents folder on your Kindle.
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