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If I understand this right--and I was just asking a similar question in another thread, so I hope Kovid will correct me if I get it wrong--when you save the files to disk from Calibre, it puts all your new metadata into a .opd file that it stores along with the mobi file. If you then Add that file back into Calibre (don't drag and drop, but use the Add File command), the data gets read and incorporated into the book file at that time--to the extent that the file format supports it.
I don't fully understand the reason for requiring the extra step. I wonder if this might be a place to suggest an enhancement, so that Saving a book file to disk would incorporate those changes, where possible, into the book file in one step.
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