You can't disable or modify sync settings on Windows Server 2016. There is no "Sync your settings" option in Settings -> Accounts.
Customers who have deployed Enterprise State Roaming to their Windows 10 users will see those users' settings roam to Windows Server 2016 if they use the same connected account when logging on to the server. Changes to roamed settings that are made on the server will sync to other client computers, such as the user's desktop computer, and changes made on the desktop computer will sync back to the server.
An image for a desktop background or a specific theme will sync to all devices, both PC and server.
The relevant setting, although present in Windows 10, is missing in Windows Server 2016, so the setting can't be disabled through the Settings menu.
We recommend that administrators use one of the following methods:
- Use a separate account to manage servers that is not configured for Enterprise State Roaming.
- Enable the following group policy on the server:
Computer Configuration\Administrative Templates\Windows Components\sync your settings\do not sync