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Regarding 2) I expect that the files WERE restored to the calibre library, but do not show up in the Calibre GUI because they are no longer referenced in the Calibre metadata.db database. One of the options in the Library Maintenance (after checking the metadata) is to look for a mismatch between what is shown in the Calibre GUI and what files are stored in the underlying file system. This allows you to find and correct such mismatches, and is quite likely to result in you finding your 'lost' books.
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