The latest Calibre  update launched today, and it was interesting enough that I had to try it out. He’s added a “Polish” option.
New tool: “Polish books” that allows you to perform various automated cleanup actions on EPUB and AZW3 files without doing a full conversion.
Polishing books is all about putting the shine of perfection on your ebook files. You can use it to subset embedded fonts, update the metadata in the book files from the metadata in the Calibre library, manipulate the book jacket, etc. More features will be added in the future. 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 Polish books is a completely new codebase, so there may well be bugs; polishing a book backs up the original as ORIGINAL_EPUB or ORIGINAL_AZW3, unless you have turned off this feature in Preferences >Tweaks, in which case you should backup your files manually. You can also use this tool from the command line with ebook-polish.exe.
It’s not very exciting yet. Note the limited number of “polishing” options. I tested it, and most of my books didn’t seem to need much polishing. However, there is one useful feature, if you like your book covers to show up on the Shelf View of your e-reader or app. You can select all the books in your library without covers and add them using Polish. That’s a nice feature. Previously, to add a cover that would appear in Shelf View, you had to perform a complete reconversion. (Just updating metadata didn’t do it.)