I suggest to esblish first your new SEPM server (SEPM 12.1 RU3) then create an install settings in admin tab, then select Install Packages.
In Install Settings, you can create or add another settings. In Basic Settings tab, select the "Remove all previous logs and policies, and the reset client-server communications settings".
Then, create an installer package with the install settings you've created. Deploy the Installer package to the SEP clients with 12.1.671.4791 version and it will automatically upgraded and report to your new SEPM server.