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FWIW the epub3 spec only recommends a folder but does not require one. So a valid epub3 may have all of its files in the root of the epub zip.
As DiapDealer recommended you may want to run"
"Tools->Restructure Epub to Sigil Norm"
after loading this epub, so it forces things to go where you probably expect them to (the places old Sigil forced them into).
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