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According to your log, epubcheck ran to completion and found a bunch of empty "id" attributes. It also found some missing files and missing targets fragment. So the parsing of the epubcheck output must be an issue but what looks so strange here are the file paths have path joiner set to "." instead of the normal "/" character. I am not sure if that is the issue or not but since file extensions and "." are allowed in file names and directory names, it will cause serious issues when trying to parse a path.
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