Is it possible to update the certificate used by Remote Desktop Services on Windows Server 2012 R2 while users are connected in RDP without disconnecting every one ? I think that it will be transparent for the existing connections, and that the new certificate will be used for new connections but I'm not sure.
Your assumption is correct. Active users will use previous certificate until they reconnect or security transport re-negotiation occurs. In this case certificate change will be transparent for users.