There are also other entrances. Some are easy to find, like the main one that the farwalkers use, and some are various caves, that the gang often find. Like ones seen in various episodes.
But the question about the flying sharptooth is a good one. Likely it's like many other things in the movies, where a char is there for 1 movie, then they vanish. Putting aside the fact that Pterosaurs, I'd guess, were not plant eaters, though I'm no expert on animals, certainly not extinct ones that lived in the distant past.