game is fubar now

I logged out of the game and left my server running so a friend could play. When I came home Steam told me the game was no longer installed (even though the server was still running) and it had to reinstall the game.

Now I cannot get the server to load, I use the EmpyrionDedicated.cmd with a fresh, original dedicated.yaml file, I get the DOS window message, then server gui frame appears briefly and then vanishes.

What is going on?