I think this was sort of brought up in another thread a while back; people wondered how Petrie got lost when his mother could have flown back to get him. It was suggested that Petrie's family had been up a tree during the Great Earthshake; Petrie's mother and siblings took flight, and Petrie himself fell to the ground and got obscured by something. After the Great Earthshake ended, Petrie's mother flew back and failed to find him, and thus continued on to the Great Valley. Later, Petrie ascended to the top of a tree in the hopes of being spotted, only for Littlefoot to inadvertently discover him.
As for the other parents, the fact that they moved on suggests they assumed their lost children were either dead, or weren't going to survive much longer. As a result, this also implies that the flyers didn't join with the other herds until after they'd started moving on, else they'd have been able to fly over and check.
On the other hand, it could be that they DID fly sweeps, but failed to see them for whatever reason; Petrie might have been obscured as mentioned above, Ducky may have been swimming, Littlefoot...might have been thought dead if they saw him sitting with his dead mother, Cera could have been sheltering somewhere rather than staying out in the open on an otherwise flat plain, and Spike hadn't been hatched and wasn't even a target - in addition to that, he's far enough away from the divide that his parents probably weren't involved in that, but died in some other disaster.
