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Open Calibre
Connect your kindle
Select device view (along the top)
Highlight all books on device then select the add to my PC option (sorry working from memory here as on a mobile phone)
Select a folder on your PC to send the books too(NOT a/the Calibre folder)
Once books have been copied to the folder go back to Calibre and select Add Folder
Navigate to the folder the books are in and import all the books into Calibre
This will load them exactly as they are on your kindle so you may have some work to do to get everything back the way it was.
Are you sure your Calibre library is really gone? Do you have a back up anywhere?
NB Adding to Calibre will create your Calibre Library so you can delete the folder you saved the books into initially or just keep it as a back up
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