I just had the same thing happen last Friday night.
We had to uninstall FileMaker Server 13.
After the Uninstall
1. Move the databases and backup folders to the desktop…
2. Delete the /Library/FileMaker Server folder.
3. Reinstall FileMaker 13 Server.
We have experienced this twice now!
Its not fun! Many late nights getting it back up and running… We tried to just uninstall and reinstall without deleting the FileMaker Server folder and it doesn't work. We have also tried to use the edit deployment with NO success…. Good luck!