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You can "polish" your ebooks with calibre since version 1.0. But you have to add the capability to the calibre interface:

To use this tool, go to Preferences->Toolbar and add the Polish books tool to the main toolbar. Then simply select the books you want to be polished and click the Polish books button. Polishing, unlike conversion, does not change the internal structure/markup of your book, it performs only the minimal set of actions needed to achieve its goals. Note that book polishing only works in ebooks in the EPUB and AZW3 formats.

Once you have added the button to the toolbar, you select EPUB books and then the "Polish books" button:

If you only select "update metadata..." you should get what you want in the EPUB files.

If you are running on Linux with Gnome, the polishing of many (50+) books can overflow your notification application. This is because polishing is done faster than the time a notification is displayed.

To resolve that problem you can use the find based solution by Simon, but that always updates all epub files. The method described in this answer only updates those .epub files for which the metadata has been updated by Calibre.


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