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No - you cannot change the way calibre names files/folders inside it's library. You can, however, control the folder/file naming style that is used if you export a book from the Calibre library via "Save to Disk" or "Send to Device" by altering under Preferences the masks used.
It sounds as if you are re-adding the book after changing it? That would explain the number changing as you are creating a new database record. If instead you add the book via the Edit Metadata dialog for the existing book entry this will not happen.
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