Hyper-V Replica allows you to configure where replicated virtual machines will be stored. You can either choose to have all replicated virtual machines stored in a single location, or you can choose to specify a separate location for each primary server that is replicating to you.
But what if you need to have multiple virtual machines replicating from a single primary server, but stored on different drives?
This is what I needed to do for my home configuration. It turns out that while the solution is not obvious, it is not that hard to do. What you need to do is:
1. Configure Hyper-V Replica to store the replicated virtual machines in one of the locations you will be using
2. When you enable replication on a virtual machine that needs to be stored in a different location, choose to perform initial replication at a later point in time:
This will mean that only the configuration file and some placeholder virtual hard disk files will be created at this stage (all of which are very small)
3. Go to the replica server and find the virtual machine in question
4. Choose to move the virtual machine
5. Move the virtual machine storage to the location that you want for the replica
6. Return to the primary server and choose to start initial replication
When you are done you will have the virtual machine replicating to a unique location. (Ben Armstrong’s Virtualization Blog)