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I'm guessing InDesign is including obfuscated fonts in the ePub and Book Proofer is mistakenly considering the entire ePub as being encrypted rather than just the embedded fonts. I know next to nothing about InDesign and I've never even heard of Book Proofer, but maybe someone who has can shed some light on whether Book Proofer barfs on obfuscated fonts or not. I'm fairly certain I've heard others mention that InDesign obfuscates by default.
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