Like theducks said, you will have to copy your newly editted ePub to Calibre. Usually, what I do is delete the old book completely from Calibre then copy over the new and improved version. When you copy it over, if you havent changed anything else, it should still have all the other modifications that you made to the book (Author, Title, date, etc.).
P.S. I also want to say if you opened the book directly from Calibre through the open folder option, it should also save it in that exact folder, so you shouldn't have to copy the new version over. Just make sure you don't convert the old version back to ePub or you will loose all your work. Take that from a person thats done it to many times to count and lost many hours worth of editting
