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You should NEVER do anything (other than BACKUP) to a Library FOLDERS contents, Calibre is the Log IN and LOG out (delete) record.
Your wanted Keyword: Auto Add folder . That is where you place books to be discovered by calibre. Calibre will then move them into the Library doing all the steps IT needs to process.
What Calibre can't do is supply missing or correct improper metadata. You can have Auto Add mark entries (for human review?)
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