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If it follows the core calibre logic (when converting and polishing) I believe the "original_epub" is used as the source for all changes, if available. So if it doesn't exist, calibre changes "epub" and backs up the original as "original_epub", but if it DOES exist, calibre uses THAT as the source for the conversion/polish, and overwrites the "epub".
Under no circumstances is "original_epub" ever supposed to get overwritten.
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