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If you update author or title, then that information is used to give path and filename of your books. However calibre takes some liberties with the metadata. Characters are replaced and the items may be truncated to ensure that the path and filename is valid. And since calibre is cross platform, calibre is rather strict when replacing characters. Also a number is added inside parentheses.
The folder and filenames are automatically updated when you change author and title in the GUI. No need to save anything.
If you can't see the effects of the update, then you are looking at the wrong place, are mistaken about the current metadata or your calibre library is corrupt. Or perhaps all of this at the same time.
You typically shouldn't access the books from inside the calibre library. Instead use the GUI or save the books to an external folder using the save to disk template. If you access the books directly in the calibre library, then you may make the library corrupt.
As has already been suggested, run the library maintenance tools to ensure the library is OK.
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