I think it's probably just that they thought he was dead. We don't know whether Petrie's family was moving with the others towards the west (meaning Petrie would have needed to have been carried by his mother), or whether they normally lived where they did, but either way, by the time of the earthquake, Petrie was unable to fly.
The tree Petrie was in when he first made his appearance was probably his family's nest. In the earthquake, which took place in the early morning, Petrie and his family would have been shaken awake. Petrie would have fallen out of the nest (as he mentions when he meets the others that he climbed the tree he was in), and been lost somewhere on the ground. The ground may also have shifted as he fell, sweeping him away and making it appear that he was dead.
Because his family were capable of flying between the divide, they must have come back to search for him, and after failing to find him, assumed that he died and joined the others moving west.
Meanwhile, Petrie, who managed to return to his nest or nearby from wherever the earthquake took him, clambered to the top of a tree, knowing that not only was he safer up there, but that his family might return for him, or at least, they'd have a better chance of seeing him up there.