Deleted files, now only have books on kindle

Is there a way of putting all the books back into calibre

I've tried to copy and paste via kindle docs of my files directly into calibre but it doesn't work, loads the path rather then digest the book properly

I had it synced in a Dropbox folder and made a mess as I was attempting to create collections to manage it better but accidently hit delete in calibre. And then my Dropbox started syncing. I managed to pause but now calibre is empty.

I have copied the books from the kindle root directly into the calibre directory in the mean while.
Again nothing shows

I hope you can help

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