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Sigil shows this message when it detects the presence of an "encryption.xml" file in the META-INF folder. This file is placed there only when the creator wants to encrypt the content of his epub. Are you saying that InDesign places an "encryption.xml" file even when the epub is not encrypted? That would be an interesting move by Adobe; extremely stupid, yes, but interesting nonetheless.
I'd like to see that file. Feel free to create an issue on the tracker with the epub attached.
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