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EPUB supports the most metadata. However, no format supports all of the metadata that you can enter into calibre.
calibre only writes metadata to a file when you use Save to Disk or Send to Device. This is so it can have more metadata about the book than what the format the book is in supports. Also this is much faster than writing metadata every time you make a change to every format you have the book in. Some formats have to have the entire file extracted then rebuilt to change metadata.
If you want the file itself that is in calibre to have the updated metadata you will need to enter the metadata into calibre, convert the book to EPUB if it isn't already. If it is already in EPUB then you will need to do this extra set, use the Save to Disk option to save the file out of calibre. Use the metadata editor dialog to delete the EPUB file for the book then add the EPUB you've saved back into calibre.
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