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The only way any books get deleted and sent to the wastebasket is when you use the remove books feature. Restoring them from the wastebasket will not add them back to your library.
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This was a previous problem. I had added 3 books, and Calibre told me it had finished, but when I looked the entries were there with no formats against them. I checked the folders and they were empty, so I thought I would delete the entries and re-import them. I selected the 3 entries and deleted them, and found that another 115 books had gone as well - no way I could have selected them by accident.
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Although folders come and go all of the time as the metadata changes the folders/file names change too.
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In my case folders seem to come more than they go
The opposite is true of books
