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The Save to Disk option is irrelevant in your workflow. Think of it instead as an "export to disk" option. You seem to be thinking of it as an Update books inside Calibre library which it is not.
To get your metadata changes applied in your scenario you need to run a conversion in calibre (even if both input and output formats are the same). Without doing that you will be getting the books in their unmodified form (I.e. Exactly as they were before you added them to calibre). Metadata is only updated in the physical ebook files on conversions, save to Disk (export) and send to device actions. There has been discussion about providing a way of updating the metadata in the files inside calibre's library 'in situ' without conversion but currently that does not happen. (for reasons probably too complicated to go into here)
Having said all the above you could achieve the same effect by doing a Save to Disk to get the files updated, and then read the saved books to Calibre as the new versions of a format would then take precedence. However it is easier to do a conversion of a format to the same one as mentioned above.
Note that if you were using iBooks instead of Stanza then calibre has full integration with iTunes, and the conversions would not be necessary as calibre would update the metadata as part of the transfer of books into iTunes.
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