You know what I think? I think that, when the Ellimist saved Elfangor from his fate as a human nothlit, he simply didn't return his morphing powers. Think about that. The Ellimist only said that he would return him to his past life, not that he would have morphing powers again. Plus, it's never mentioned that Elfangor tries to morph ever again after being returned to Andalite form. One could even go so far as to assume that the Ellimist made it so Elfangor couldn't regain the morphing power. Elfangor may have thus been the equivalent of an Andalite nothlit.
And it would have made sense for the Ellimist to do this, too, because if Elfangor could still gain the morphing power, what would stop him from going back to earth, finding Loren again, and going back to how things were? Since the Ellimist wouldn't want that, he might have taken measures to made sure that wouldn't happen.
So, to answer the question, I think that Elfangor didn't morph because he couldn't.