How to modify an epub with the Calibre database informations ?

When I modify the metadatas of an epub in Calibre, my modifications are only stored in the Calibre database but the epub file itself is not modified.

I would like to do that to have "clean" epubs if I have to restore my epubs in a new installation of Calibre later.

So, is it it possible to modify all my epubs with the Calibre database metadatas and if yes, how ?

I found a work around by "converting" my epubs to epubs. That creates a new "clean" file and rename the original epub with the extension .original_epub . The problem is that double the size of my Calibre directory.

Is there a better way to do that (I mean without keeping the original file) ?

Thank you !