Niantic calls their database Lightship.
You might be familiar with the submission map. It shows all accepted wayspots, even the ones that do not appear in game as @AliceWonder1511 has pointed out. Here’s a brief article on the topic.
It’s a question of whether it only does not appear in Pokemon GO or has been entirely removed from the wayspots map that is unclear with your initial post. The details of the wayspot in question should enable us to check and give advice.