Epub format is, essentially, a zip archive containing a bunch of human-readable, text files. Unzip the file twice to create two copies, it should be a 15 minutes job with any text editor to fix the copies, if you know what you are doing. If you haven't tried it yet, an excellent starting point is
Epub Format Construction Guide.
You need to identify xml/html files that need to be removed/edited, and then do a couple of simple modifications to *.opf (remove entries related to xml/html files that you are removing) and toc.ncx (remove entries for files that you don't need, reorder the rest) file. Once you're done, zip the files to create new ePub containers and test them. That's it.