I make new co-op game and copy game files to Saves directory of dedicated server (how did it before). Also made minor edits to dedicated.yaml. The problem is that the server does not pick up the settings from the gameoptions.yaml file at startup. Has something changed in the new build?
The issue is resolved with EmpAdminHelper. With it, I turned off the server, edited gameoptions (at the same time, gameoptions.yaml was edited, which already contained normal options), and after starting the server picked up all the settings. Some kind of magic.
