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Calibre keeps track of the books and folders using a database. If you add, delete or restore books manually in the Calibre Library folders, and don't update the database, you are bound for trouble. Don't do it!
Treat the whole Calibre Library folder as a singe black-box object.
Use only Add/Remove/Convert from within the program to make sure the database is in sync with the Calibre Library. Othervise you WILL MOST LIKELY loose data and corrupt the Calibre Library, as you have noticed.
This is not a bug.
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