Next time do /stop to close the server instead of just closing it. It will save all the chunks and worlds.
The central island of the end has a bit of a special behaviour. It's not really modifiable since the structures will respawn. There might be a way around it, but not with the regularly created end. If you wanted to do something custom you have to do that outsite of the perimeter of the isle. I have not idea how large it is but next to the generated islands where the cities spawn should be fine.
