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The problem is that most file formats dont support much metadata, so you can't "finalize" the metadata to be all the metadata in the calibre database since the file format does not support the metadata at all.
calibre supports writing metadata to MOBI, EPUB and LRF files. So when you save to disk, the metadata in those files is updated to reflect the metadata in calibre *to the extent supported by the file*.
Which is why saving a file and re-importing it is not going to give you correct metadata beyong title and author and maybe publisher.
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