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So this is (I hope) the definitive explanation for how metadata works:
1) When you make changes to metadata in calibre, it is stored in the database, but the book files are not updated.
2) When you use either the save to disk or the send to device functions the metadata *is* updated, but only in the copies (i.e. in the newly saved files). The files in calibre's library are still not affected.
3) Because different ebook formats support different amounts and kinds of metadata, the only complete set of metadata in te "saved to disk" files is in the OPF file. I cannot overemphasize just how dicey this process is. For example different generations of PRC files support different amounts of metadata. The same is true for LRF files. This craziness was what prompted me to make the decision to store metadata in a database in the first place. Even EPUB doesn't support the full set of metadata in the calibre database.
4) Instead of re-importing the saved books with the metadata into calibre, you should use the edit metadata dialog to just re-import the specific format.
5) When you do a conversion, it will use the latest metadata from the database, so your newly converted file should have as up to date metadata as possible. In many cases, this will result in a file that has superior metadata to one for the "Save to disk" process. This is because calibre generates the most modern version of each file format, with the greatest support for metadata. But it is important to understand that even a converted file will not have all the metadata available in the calibre database.
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