Several trainers had been reporting that Pokestops and gyms have just disappeared from their maps. However, in some cases, this is due to them being removed from the game but not all cases. After twitting to Niantic’s newest support account. Niantic was able to solve the issue.
It turns out there was an intermittent server issue meaning the bug isn’t continuous. Thanks to reddit user MatroRedditz and other reports of disappearing gyms and Pokestops, Niantic was able to look into it further and fix the issue.
If you have any issue with the game. Don’t forget to visit Niantic’s support website or twitter account. They have been trying their best to listen to the community and help where help is needed.
Tweets by NianticHelp