I don't think that's a supported workflow. At least, I've never heard of that being possible. I think you either are going direct from InDesign to EPUB, or you're using iBooks Author. But I've never used iBooks Author so I can't speak with great authority.
Would this be of interest?
"Apple has updated iBooks Author for OS X Yosemite and added support for new file formats and other enhancements. First among these is the ability to import Adobe InDesign and ePub files to a project. New blank templates have been added to accommodate custom designs, and authors can now use hyperlinks to jump to a specific location in other book or add a link to an image."
Apple's iBook Proofer is a fast way to proof reflowable EPUBs on your iPad or iPhone but doesn't support the font encryption that InDesign does even though it's valid. You'll need to re-export from InDesign but turn off "Include embeddable fonts" during export if you want to use it.
However, with Mavericks or Yosemite (10.9/10.10), iBook Proofer is far less necessary than in previous versions of OS X, since these later operating systems come with iBooks as a full-fledged program on your Mac. Before it didn't, so people used iBook Proofer instead of synching constantly with iTunes in order to get new versions on the iPad to proof.
iBook Proofer has nothing to do with iBooks Author, which is Apple's authoring program for creating their own proprietary ebook format called an iBook.
If you are actually trying to get an InDesign file into iBooks Author (like it can import a Word file), then you need to export your InDesign file to IDML. Honestly wouldn't see the point in exporting ID to EPUB and then importing the EPUB, but I might be wrong, I haven't compared or tested the two methods. Your book will look really differently as an .ibook than as an .epub.
Thanks for the clarification about iBook Proofer history. Sounds like I don't have to use it and should just proof my iBooks Author work directly on the iPad via the cable