I've been using Desktop 10.3.1 and Server 10.3.1 to replicate an sde geodatabase. Here are the steps I took. Add GUIDs, enable editor tracking, register as versioned, export to xml --> copy to azure vm, load into sde, register as versioned, publish geodata service, add datasets to new mxd on VM, publish map as map service to the same location as geodata service and with the same name, ---> On local machine add map service to mxd, use the distributed geodatabase toolbar to create a 2-way replica to the local sde geodatabase.
The creating replica window has been active forever without any sign of ending.
I've been experimenting with different methods and so far I have not been able to register existing data as a replica.