Jurassic World 'WHERE DINOSAURS COME TO LIFE' book.

In the book, they had an aviary in the park (although no Pteranodons, but an other species of pterosaurs, Cearadactylus). It wasn't planned to open with the park - due to the Cearadactyluses, wich proved to be much more territorial, than the scientists of the park thought them to be -, but it was there.

It's more than logical, that they had an aviary in the movie universe too, or at least they had concrete plans for it, because

A: as you said it they, had Pteranodons on Sorna,

B: in the lunch scene where Hammond says some attractions will open later there is a concept art for it on the slides in the background,

C: In The Lost World, there is that promotional image for Jurassic Park in the worker village, wich features a pterosaur in the top-left corner.

Much like the Rides, the aviary hadn't finished completion yet, And were scheduled to come online a few months after the Tour. According to hammond.

So, with that in mind, it was probably near finished, and with nothing there to potentially wreck it from the inside out, it most likely stayed in fair condition. KEEPING IN MIND, that Dr.Wu and a team returned to clean up the island a year or so after the accident. 

In the third JP Universe (Jurassic park the Game Universe) There was indeed pteradons on Site A, but they had yet to be fully integrated into the park. 

I'd be interested in seeing how is plays out in the end.