If all you want to do is CHANGE a cover image.: Tweak is probably for you.
In the Library: select book, tap the T key.
"Explode_epub" the book.
Locate the existing covers filename (it may be in a top level or a folder).

the file browser thumbnail view may show the image.
Delete that file and replace it with your
new file in the same folder you found the OLD version.
Note:
The new file must be of the same image type and you must use the
exact (including case) filename.
(back on the Tweak_epub control window) "Rebuild_epub"
Enjoy your new cover