He does reappear after all the bad things start happening in Tri. Taichi runs into him, and it's revealed here that Daisuke no longer believes in miracles. To emphasize this, the crest that he received at some point before the final battle with BelialVamdemon not only doesn't glow, but has gone completely grey. He says that because of this he can't fight to help. Taichi will later find Jun and bring him up and explain his tenure as a Chosen Child and how he was the Child of Miracles, but that he no longer believes in miracles. Jun will start crying and explain that his very existence is a miracle, and that he was born premature and not expected to survive. According to her, his survival didn't encourage their parents to form an attachment to him, afraid that they would start to care and something would happen to him. Jun followed her parents' example, thinking it was the appropriate thing to do; it was only after he disappeared that she discovered that isn't the case and that she missed him horribly.
Taichi takes all of this info back with him and talks with Hikari and Takeru, and Taichi susses out that Daisuke didn't just have a crush on Hikari by the end of the adventure, but outright was in love with her. Takeru agrees that all of that taken together makes his decision to disappear make perfect sense. Later when talking alone with Taichi, Hikari says that there's nothing to be done about it, as her feelings aren't going to change for a person that she no longer even knows, even if they do need his power to overcome what they are up against.
From there, I don't know what to do. My brain toyed with the idea of someone getting sent back in time, possibly even Hikari, to relive the second adventure and make different choices regarding Daisuke. But I don't know. It feels like a cop out, but then again, I don't know what else to do with this story... I suppose it depends on what is coming up in the next part of Tri.
And that's it. I think I've got as much on this as I'm going to get at this time. I'll revisit this if the rest of Tri forces any changes to this...