I'm not sure when this started, although definitely before the last two test versions, but on AO3 downloaded stories, the author link is cut. The url shows as follows:
Code:
<a class='authorlink' href='/users/Rivalry_of_Destiny/pseuds/Rivalry_of_Destiny'>
You'll note the "http://archiveofourown.org" is missing.
I downloaded test stories from ff.net and tth.org, and in both of those the author link shows up properly.
I also took an existing epub that had the authorlink, updated it (update always) and it changed the link so the http part was removed.