It's distinctly possible that he said he's not working on it because he simply hasn't been approached yet. The game is still early in development, too early for music to be a high priority.
That said, I'm not really worried about the music even if he doesn't return. Square Enix owns the songs from the original game, and while fresh blood might not be able to capture the magic the same for new compositions, music has generally been one of the company's strong points even in their worst games, and there's nothing stopping them from having new musicians arrange Uematsu's old music while still keeping the charm.
Personally, if Uematsu doesn't end up returning at all, I would like to see Falk Au Yeong do the music. With Square Enix he's only ever done mixing/mastering/recording engineering, but I've heard some of his original compositions for other projects (mostly Sonic fangames), and he is truly talented. But since he's not Japanese, there's no way they'd ever give him a major creative role.
