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Did you ever do anything to save the tags into the actual book metadata? If you did there should be a way to extract the tags from the individual book metadata, though it might take some trial and error to figure out the best way to do it in bulk. The bulk modification you did would only affect the Calibre db.
If the data isn't in the books themselves I don't know if there is anything else that could be done - any recent backups?
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