I've got the same problem with you. I'm stucking with embedded fonts. My epub created with inDesign CS6 cannot open in Sigil if it is one document type. If epub created with book of documents in inDesign, it's OK. Maybe I have to back to CS5.5 in order to open it in Sigil to embed fonts.
Is there a way to embed fonts after exporting epub by inDesign without using Sigil ? I've tried many ways I've Googled but they didn't work.
Need help seriously.
As usually adobe gives crappy software full of bugs and charges lots of money for it. No there is no way. Something between 5.5 and 6 went wrong.