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I just skipped the tech talk on this one to answer...based on what you said..you exported the files in a group and not the entire folders individually.
It sounds as if you didn't update the metadata in the files. If you are just importing individual files, it will pull from the metadata in them. If it was never updated, then you won't see your fixes. Calibre doesn't do this automatically. You have to update the metadata for it to be "sealed" in the file.
I hope this helps.
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