Metadata is not embedded into ebook files merely by updating it in Calibre. The ebook files are updated if you use 'Send to Device' or 'Save to Disk' options. You can also update the ebook files in-situ using the 'Polish Books' feature.
It sounds as if you simply copied the ebook files from the Calibre filestore using the OS level copy facilities. This would not have updated the metadata.
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