The relative link " <a href="../REFERENCE/anotherbook.pdf">another book</a>" will be relative to the *parent* file path of "goodbook.epub", i.e. "Documents". The link you want should be relative to "goodbook.epub" itself instead of its parent, i.e. " <a href="./REFERENCE/anotherbook.pdf">another book</a>". Notice that there is only one dot at the beginning instead of two. Still don't know if it will work, but at least the link should be correct.
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