Pretend Calibre's files don't exist. They are part of the database and not intended to be accessed directly! The Export/Save to disc functionality lets you have any filename you want. See Plugboards (?).
With Kindle, Sony and Kobo ereaders the filename exported is also irrelevant as the native readers use metadata, databases and library interfaces.
The filename only matters when export/copying to something that uses a file browser / manager to load a file to read.
Calibre also isn't a conventional "library", it's more a catalogue and ebook for ereader management system.
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