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FWIW, inside Sigil all fonts are unobfuscated so that they can actually be used (ie. you are not looking at garbage in Preview). Only when saved are the fonts obfuscated and the encryption.xml added.
So the epbcheck plugin run on the epub when open in Sigil would not see any encryption.xml but epubcheck should have still warned you about the out of date mimetypes being used on your fonts (ie. non core media type). I guess epubcheck does not bother to run that check if you are not obfuscating that font.
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