Changes in metadata is usually only stored in the database metadata.db.
It is only written to the actual ePub when you send to device, save to disk or do a conversion. ePub to ePub for instance.
You can also get the plugin "Modfy epub" to update the metadata inside the ePubs.
The reason for this behaviour is that it would make Calibre very slow if every small change of metadata had to be written to the ebook. It would involve making a copy of the book, unzip it, change the metadata, zip it, and replace the original ebook and finally delete the copy. It is much faster to only update data in the database.
Besides, you should really not look inside the Calibre library. If you feel a need for it, then you are most likely using Calibre the wrong way.