I'm glad you have come across the Modify ePub plugin as it seems to accomplish exactly what you're looking for.
Quote:
Originally Posted by krimhorn
Upon making changes to the metadata it saves covers in the folder with the book and the metadata in the .opf file.
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The .opf files you see in the library structure are used strictly for reconstructing the calibre database should it ever be needed.
Quote:
Originally Posted by krimhorn
This would be fine, except I need these books to work with a reader that does not support getting the books from Calibre (at least I assume that if I used Megareader/Quickreader to import the books it would get the correct metadata).
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Any feature in calibre that exports the books will also update the metadata. Most folks use Send to device and you know about Save to disk, but you may not know about the Connect to Folder feature that allows you to connect calibre to any folder and treat that folder as a device. Once you are connected to a folder you would use the Send to device button used for sending books to any device to send books to the connected folder. Another method would be to use the content server which updates ePub and Mobi metadata as it serves the the book.
The reason calibre doesn't update the library copy is because calibre doesn't support or encourage direct access to its file system. Calibre has provided multiple ways to export books from the library that should serve well.