Updating Your Server
Keep your server version in sync with the client.
SteamCMD Command
Conan Exiles Dedicated Server App ID is 443030.
steamcmd +login anonymous +force_install_dir ./conan_server +app_update 443030 validate +quit
Mod Updates
Updating mods is harder manually. You usually need to download the .pak files from Steam Workshop or use a script that supports mod updating (like DedicatedServerLauncher on Windows).