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Calibre maintains its own database of detail on a book, adding entries as the books are imported. Changing any of the metadata (title, author, tags, ... , and even the cover) in calibre does not make the change to the actual ebook files, only calibre's database.
When you export an ebook though one of the proper methods (Send-to-Device and Save-to-Disk) some of this data gets updated in the ebooks. When you convert ebooks all of the calibre changes get updated in the newly converted book, but not the source book.
There is also and Modify EPUB plug-in that you can add to calibre that provides a method to easily write the calibre changes back into the original ebook.
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