1. Stop the server.
2. Remove all world files from the server.
3. Set the server world name from Web Interface to match the world save you wish to use.
4. Move the world file to the server with its original name (do not rename the file).
5. Start the server.
I had to go through this process 4-5 times until it worked properly. Additionally, if the world name has a space in it, that might be causing issues as well - at this point rename it prior to anything .. and make back-ups before applying any changes to the file.