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Missing books can be caused by 'messing beneath the skirts' either directly (using Explorer) or because you placed the Library on Google drive or some other cloud/NAS
GD renumbers the FILES as part of it doing history. That is 100% incompatible as Calibre also uses numbers as part of the file name and those no longer can be found since someone or something changed the file name and it no longer matches what is logged.
BTW formats:false WILL NOT find these as missing .
You must use Library Maintenance, which actually checks against what the DB has logged
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