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Regenerating the EPUB, I assume with Modify EPUB, is useful:
If you want to embed/update a jacket.
Or if you will be accessing the files through the filesystem/dropbox/calibre2opds. Since you will not have calibre handing you an on-the-fly updated copy, you need to ensure the master copy is up to date. And you won't get the use of plugboards.
If you are only updating the metadata, you may want to use the Embed metadata tool, which updates the library copy of all formats with the same procedure that send-to-device uses. Polish/Modify create backups since they can also subset fonts, force-insert a (missing) cover -- not just updating the cover.jpg inside -- and create or update a metadata jacket "chapter".
But even this doesn't activate plugboards.
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