You know how Clearsight put the sleep bracelet on Darkstalker, even though he wasn't going evil because of the scroll? Clearsight could not have done that for no reason, unless Darkstalker actually was going evil.
Prolonged exposure to the Animus scroll or any type of Animus object might be able to cause a dragon to go evil. Darkstalker might not be currently evil however, as over time the effect would likely wear off. If that's true, when Darkstalker remembers what happened 2000 years ago, he would have remembered what he thought when he actually was evil, which would probably cut out the things that actually were, and he would believe 2000 years ago he was innocent, when he remembers now what he thought 2000 years after, he would remember how he felt then.
That, or the effect never actually wore off, but I think that Darkstalker probably isn't evil in the books currently, as he told Moon to destroy the scroll if she ever found it, even if she didn't rescue him before the scroll was destroyed.