Simple answer: we (the readers) have no idea what may have happened to him. Scourge took on his current form after the original Mobius: 25 Years Later, which ran from issues 131-144; Evil Sonic became Scourge in issue 160. In the second 25 Years Later, issues 166 and 167, the story focused on Sonic, Knuckles, Tails, Lara-Su, and Shadow to the exclusion of all but a handful of other characters in the comic. Additionally, much of the history in both timelines is unknown to the readers because it simply hasn't been explored or explained in the story. Scourge might have died, gone home, or had anything happen to him.