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If check library does not report extra folders then one of two things is true:
1) they are in the calibre database somewhere.
2) you are mixing case sensitive and case-insensitive file systems.
For number 1, you can look for the paths by creating a composite custom column (column built from other columns) that contains the full paths of every format file for the books calibre knows about. The template to use is {:'formats_paths()'}. After you have created the column, search for one of the books you think is not in the database.
For number 2, I am not sure what to do other than not to do that. For example, if under Linix you create a file "foo" and "Foo" then there are two files with different names. If you later look at the containing folder with windows then strange things might happen.
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