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Use the Library Maintenance->Check Library tool, it will match the library subfolders to the database author and book tables and report discrepancies. Some may be fixable, others may require you to move sub-folders elsewhere and re-add the books.
This sort of problem is almost invariably caused by using a file manager to alter the library contents, i.e. deleting and renaming folders and files etc. That's a no-no with calibre. To maintain coherence between the database and file system all changes must be done in the calibre library management application - e.g. via adjusting the Author Name and Book Title metadata .
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