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Where is your library located? The symptoms you describe suggest it could be something like a NAS, or a cloud service such as Dropbox. Both of these can interfere with Calibre’s internal working. Also Google Drive can silently rename files/folders causing Calibre to lose track of books.
Have you tried running the Calibre Library Maintenance option? This can identify cases where you have books on disk that are not correctly registered in the Calibre database.
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