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This message usually happen if something is blocking calibre to change a file.
Possible candidate's are AV, a program that block a open book (situation e.g. import a pdf, editing metadata and parallel open the book with Acrobat for extracting data, forgot to close the book and try to save metadata) or tools like CCleaner that clean up automatically temp files after closing a web browser while calibre is actually fetching news or converting a book). Things like that.
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