I wasn't explicit about it, but I meant for you to open the files in a text editor. If they are readable and show the tags, then it probably isn't encrypted. But, I'm expecting that they are and you will see a random set of characters or the text editor will refuse to open it because it is a binary file.
If nothing appears to be encrypted, then open the ePub in either the calibre editor or Sigil. See what they think. And run the error checking routines.
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