Q: I want to use Hyper-V Replica with a SQL Server instance running in the virtual machine. Is this supported?
A: The first question I'd probably ask is Why? SQL Server has its own replication technologies, such as database mirroring and more recently SQL Server AlwaysOn, which provide application-aware replication that's superior to Hyper-V Replica's application-independent replication. If you can't use the native SQL replication technologies and want to use Hyper-V Replica, it's important that if you have multiple virtual disks associated with virtual machines, the disks aren't at different time states. All disks must be replicated at the same point in time to ensure that the database disk isn't time skewed from the log disk. You can use PowerShell to make the following configuration change:
Set-VMReplication -VMName <vm-name> -EnableWriteOrderPreservationAcrossDisks 1
Note that once you use Hyper-V Replica, you can't use native SQL Server replication technologies such as database mirroring, log shipping, and so on as it would result in a broken state. For more information, see the Microsoft Support article "Support policy for Microsoft SQL Server products that are running in a hardware virtualization environment."