Oh goodness, that's a problem. -_-
After you meet Giratina in Shadow Valley (after you beat the main game), you visit the four dragon gods in their respective locations (Mount Krystal, Hell's Pit, Breeze Island, & Mount Leon). After defeating them in battle, they disappear, talking about how they are 'fading away and loosing air'. During the final event (Time's Edge), the Dragon Gods say something like, "Even in death, we are effected by our time's disappearance".
Doesn't that suggest that the Dragon Gods are dead?