TL;DR: World erased and then changed during testing how uptime and downtime worked.
Today, I decided to make a server, with a predetermined seed for oceans and islands. I was playing on the brand new server today, with a few friends. It was in an ocean, with several islands. After getting some wood, I went to a smaller island, flattened it, and built a sandstone monument. Then I had to leave.
When I returned I performed tests on the server to see how leaving would impact how server uptime worked. So to force it to turn off, I hit "Stop Server", and then went to see if the server would turn on automaticlaly when i joined. It did not. So I turned it on manually, and the world was erased and changed into a different but similar seed. The island with the momument disappeared, and was not at the coordinates I marked down for it.
I did this again to see what would happen, and it did not change this time and I was stranded in the ocean where I left it last time.
Was it my bad choice hitting the "STOP" button instead of letting it run out? Is this intentional?