Sigil WILL NOT save an ePub without the META-INF directory and the file container.xml. I took an ePub, delete META-INF, loaded it into Sigil and saved the ePub. META-INF an container.xml were both recreated. Not having META-INF is something you've done after saving in Sigil.
Just load this ePub into Sigil and save it back out and it will be fixed.
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