The most important thing to know about backing up virtual machines running on top of Hyper-V, is that Hyper-V requires Hyper-V Integration Services to be installed at all times inside of each VM, regardless whether it’s running Windows Server, Red Hat, Debian, Ubuntu, Suse, Oracle or CentOS.
Live backups are quite complex in nature. The host utilizes VSS which then contacts each VM separately through the Hyper-V Integration Services and their communication paths, see Hyper-V VSS Writer Description. Hence, without proper installation and configuration of Linux Integration Services, you can’t create live backups without interruptions (VMs will move into a “Saved State” temporarily).
In addition to installing the required services, you may also want to have a look at 18 Hyper-V Pitfalls You Need to Know and the article “4 Things You Need To Know About Integration Services“. Both articles provide further information on the general subject and the relevance of background services for host to guest communication. Probably the most important thing to know is that these services do not update themselves. Each time Windows Update is run on the host, it’s strongly recommended to check whether a service update inside the VM is necessary. For Windows Server 2012 and later we do have a PowerShell script for that to help you automate this step. Apparently on Windows Server 2016 this will finally work automatically inside the VM.
1. Use only native virtual hardware, not emulated
2. Use the NOOP Scheduler
3. Use only static MAC addresses, as there are issues with dynamic MACs when using Linux VMs on CSVs
Specific Microsoft Implementation Details for Each Operating System
Recommended Hyper-V Backup Software
BackupChain: offers uninterrupted, live backups and much more for Windows Servers.