I don't know what happened, to tell the truth. I've tried saving an epub every which way from sunday and I can't get Sigil to save one without the META-INF.
Perhaps if you had the Clean Source settings all turned off and you ignored all errors when opening/saving, but even then I don't think it would happen. And such a malformed epub would certainly never pass the internal Flight Crew validation even if it did happen. I got nothin'.
Glad you got it fixed, though.
