The "save to Disk" feature should only be used to EXPORT a file from Calibre. Using it to save books back to the Calibre internal library filestore can cause complications as the calibre database and filstore get out of sync.
Note that if you change metadata such as author or title calibre will automatically move the book to another folder in it's own filestore. You have no control over the names used in the calibre internal library files.
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