If you have it in Calibre, try Tweak ePub (right click on the ebook and select this from the drop-down menu). This explodes the zip into its parts for you to edit and then recreates the epub. It uses the correct ZIP options when it rebuilds the ePub, so you may not need to actually edit.
There is also a
Modify ePub Plugin for Calibre, which might help if you are not sure what is wrong with the ePub.