No need to do all of that. Easiest way to modify is the following:
Simply reopen the epub file and drop the edited files in them to overwrite the originals.
Here is a quick walkthrough.
- Save your book to epub format.
- While having the book highlighted in calibre click the letter "O" (will open containing folder)
- Right Click book on epub format and select "Open With"
- Select WinRar or WinZip (I advise for winrara)
- Now you can modify any of these files however much you want.
Now you decide how you want to go about it.
You can Drag and Drop everything on a folder in your computer, then edit the files, then just drag them back into the zipped file. Voila.
Epub file edited without having to import/delete or do anything with Calibre.
Enjoy