Install Agent for Windows inside the virtual machines

Symptoms

1.  You have a clustered environment of Hyper-V hosts and virtual machines are replicated from one host to another using native Hyper-V VM replication functionality.
2. You install Agent for Hyper-V on both hosts and set up backup plan(s) to protect primary virtual machines
3. When backup plan runs, either primary virtual machines or replicas are backed up, instead of just primary virtual machines

Cause

After the replication both the original and the replicated virtual machine have the same ID in WMI subsystem, which is used by Acronis Backup to distinguish VM instances. If both hosts of the cluster are registered on one Acronis Management Server and use agentless backup via Hyper-V agent, Acronis Backup is unable to differentiate between the original machine and the replicated one.

Acronis Development team is working on fixing this issue in future versions of Acronis Backup.

Solution

Install Agents for Windows inside virtual machines instead of using Acronis Backup Agent for Hyper-V. Virtual Host license allows installing Agents for Windows/Linux inside virtual machines on the Hyper-V host to which the license is assigned.

1. Install Agents for Windows inside each virtual machine running on first host and register them on Management Server

   1. To allow Agents inside virtual machines to use virtual host license click View license mapping on the Licensing step during remote installation:
      
   2. In the License Mapping window, click a machine in the Machines list:
      
   3. Under Components, examine which components on the machine require licenses.
   4. Under Used Licenses, assign any of the available licenses by selecting the corresponding check box:
      
      The Agent inside the virtual machine will use the Acronis Backup Advanced for Hyper-V you have specified.
2. Create a backup plan to back up the virtual machines using Agents for Windows. Run the backup plan to create initial backups using Agents for Windows installed inside the virtual machines;
3. Replicate the original virtual machines to the other Hyper-V host. 
4. When you start the backup plan, it will back up either the original virtual machine or replica, whichever is currently active. Backups will continue to the original backup chain without using any additional licenses.