SEP is working on with Windows Server 2012 R2, I am running with ''Basic Protection for Servers''.
Make sure that there is no changes(in PC Settings or Login Credentials) in SEP Member server while changing your Existing Domain Server.
Hope you are doing the migration(without affecting the client PCs and settings) from existing domain server to windows server 2012 R2., If less client PCs then, there are other solutions as Client Profile Migration.