You might try converting Epub->Epub before Epub->Mobi->Epub. That should generate the Original Epub format.
The only problem is that your Epub->Mobi conversion will work from the Epub that was generated from the first conversion, not from the original. That may or may not be a problem for you.
And yes, I tested deleting the second Epub format before converting to Mobi. Apparently Calibre won't let you convert from Original Epub format, unless they've changed it in the last few versions (I'm on 0.9.5).