I'm not sure the new process is documented very well, but there are new admin actions that you can call for this purpose. I'd get in touch with support on this topic.
You need to connect to your application trough SSH and use the following:
License key activation for Mendix >= 3 When using Mendix 3 or newer, use the showlicenseinformation to display the generated server ID. Using this server ID, a license key can be obtained which can be installed in the application using the activate_license m2ee command.
Please see: How To Configure your application on Linux