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Sigil used to delete unmanifested files on the next save. I seem to recall that changing because people didn't like it. I could be wrong though. But even if I am wrong, it wouldn't hurt anything to save a new copy of the epub (using Sigil's Save As) and see if the problem takes care of itself.
This sort of thing typically happens when one makes the mistake of digging around in Sigil's working directory while it has an epub open. That's something I would almost always discourage. But if the above suggestion does not work, that might actually be the simplest way to find and delete the embedded epub.
Out of curiosity: how are you determining it's 10Mb in size if you can't locate it?
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