What game? And have you made sure that the server is set to auto update, along with the option to repair files?
In that case, your server is set to check the Steam Workshop manifest for each added Mod upon restart, as well as periodically. And then install those mods on demand. As for settings, those are handled via the Basic, Advanced and Expert tabs. And the ini files should be rebuilt every time you restart the server from those 3 tabs.
What is occurring on your end that leads you to the conclusion that the updates and settings are having issues?