If you have ever converted the book from EPUB --> EPUB, then calibre will create an ORIGINAL_EPUB format with the pre-conversion state. This allows you to revert if you don't like the conversion.
All conversions, polishing, etc. use the ORIGINAL_EPUB, and overwrite the EPUB. This is to avoid converting a conversion -- since conversions are lossy, it is better to reconvert the original. That way you can change your settings if the first conversion wasn't quite what you expected.
You probably converted the EPUB and left the ORIGINAL_EPUB there. Don't do that -- if the conversion is acceptable, delete the ORIGINAL_EPUB.
Now your editing work is most likely gone.