This isn't a topic for the InDesign forum. It doesn't have anything to do with InDesign. You need to ask in a forum for people who work with EPUB regularly. The last time I checked, this was a good website:
Why? I make the epub with Indesign
Because that's not the way to make an EPUB from InDesign. InDesign has the ability to export EPUB directly either for a reflowable or fixed layout EPUB. File > Export > EPUB (Reflowable) or File > Export > EPUB (Fixed Layout).
However, you need to learn how to do it. The best source I know of is the videos on Lynda.com by Anne-Marie Concepcion. You can get a ten day free trial on Lynda.com.
Another good source of information is Sandee Cohen & Diane Burns book, Digital Publishing with Adobe InDesign CC: