I took a look at a sample of the book I downloaded from Kobo.
Code:
<meta property="rendition:layout">pre-paginated</meta>
<meta property="rendition:orientation">auto</meta>
<meta property="rendition:spread">auto</meta>
I found the above lines in the content.opf file which says that this is a ePub 3 fixed layout book.
Code:
<meta name="viewport" content="width=1508, height=2048"/>
This viewport size declaration in each of the xhtml files tells you the same thing.
Converting it to any other format is not an easy task. You will notice that every page in the book has it's own xhtml file and everything on that page is given a fixed location within that viewport.
You can use Thorium on your computer or sending it to a Kobo ereader as a kepub file to read the FLO book. Your scrambled version corrupted quite a bit of the fixed layout information and is unlikely to be viewable on anything. I'm not how well ADE 4.5 will deal with this since it's support for FLO is not state of the art.