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I know this is a very old thread, but I had the "Hyperlink not resolved" error with Kindlegen and this was about the only reference I found to it. So I thought if others come along this might be of help.
I solved my problem by first saving the kindlegen output to text (using kindlegen book.opf -o book.mobi >a.txt)
The clue was that some links in the same format were resolved, no error recorded. On examining them was reminded I had put new code after the "good" links.
There was nothing wrong with either the links or the anchors (they had worked in earlier versions) but Kindlegen was aborting reading the HTML source before it came to them, because I had inadvertently put a </body> tag in earlier, when I was pasting in some text from another project.
Probably strict HTML checking would have found this, but browsers are tolerant of errors, the entire file still displayed normally in Firefox and all the links worked.
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