Well, its happening with my coworker who is running 0.5.3 and they only thing we've found fixes it is too, convert the .epub to a .zip and then open it and open the contents.opf file and deleting a specific line of code.
Then we have to zip it back up using an apple script. It works but we cant open the file and then save it. If we do, it adds the semantics again.
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