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If they were deleted from Calibre, they should be in the recycle bin. I've found books there myself. If you have Windows 7 (I think Vista does this too), it's very easy. Just open the recycle bin, in the search field type "epub" (or PDF or whatever format your books were in), then wait. Your books should all display. Hi-light all of them, right click, select "cut." Then, create a new folder (right click on the desktop or wherever you'd like to add it, select "new" and then folder). Open the new folder, right click and select "paste." Then, go back to Calibre and click "add books," go to to the new folder, select all of them, click "OK."
Also, Calibre doesn't delete your original copies, but if you delete in Calibre, it does delete copies it manages. I.e. If you follow the method above, the copies in the temporary folder you created will still be there, even if you deleted them from Calibre, but the copies Calibre makes and stores for you in "My Documents" will get deleted if you delete them from Calibre.
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