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RDS 2016 CALs can be installed on Windows Server 2016 Licensing server. As you already has WS 2016 Licensing server, just install the new RDS 2016 CALs on your Licensing server.
As you had mentioned that, you want to upgrade CALs from 2012 to 2016. If you do not need to keep current installed 2012 CALs, you can reference below steps to clear the licensing databased and re-install the new 2016 CALs:
- Open Remote Desktop Licensing Manager.
- Right click your server name and select Manage licenses.
- Click Next on Welcome to the Manage licenses wizard.
- Select Rebuild the licenses server database and choose one of the reasons.
- Follow the wizard to complete the installation.
If you do not want to delete current CALs 2012, you can right click the server name on Remote Desktop Licensing Manager and select the option “Install Licenses”.