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One useful trick is to use the Calibre facility to move the library to a new location. That will move all the files that Calibre knows about. Those left behind are ones that are not mentioned in the Calibre database.
You could then run the Calibre Maintenance facility on the copied library. Hopefully there will not be many issues reported as the files should largely correspond to the database. The only issues likely to be of an significance are files Calibre thinks are "missing" where it has a database entry but no corresponding file. For these you can elect to either get Calibre to remove the entry from its database, or you can locate the missing file to keep Calibre happy. Having got a consistent library you can then look at the 'left behind' files and decide what to do with them.
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