If I understand correctly, you want to update the Meta-Data for all of the books that are already in your library, correct?
Looks like you'll want to use Calibre's command-line tools and create a standalone script.
Let's see, to get a list of your books (you'll need the database IDs for each one):
Then you need to get the current metadata so that you can get the ISBN number:
calibredb show_metadata [options] id
Then you'll want to use that ISBN to search for Metadata:
fetch-ebook-metadata --isbn ########
And then you take that new data and apply it to each eBook in the database by id:
calibredb set_metadata id /path/to/metadata.opf
Anyhow, I leave the details to you on how you want to script it. You could do it in Applescript if you want. Let us know how far you get!