This happens if Virtual Machine is deleted from the Failover Cluster manager and then a restore is performed.
This behavior is by design. If the Virtual Machine is deleted from Failover Cluster Manager, then the restore is like a redirected restore and so the VM is not registered as a HA VM in cluster manager.
The restored VM will be registered in the Hyper-V manager on the node which owns the Quorum. To add the VM as HA VM in Failover Cluster Manager, follow the steps below.
1- Connect to the Hyper-V cluster using Failover Cluster Manager
2- Right-click on the ‘Services and applications’ header in the left pane of the Cluster Manager and select ‘Configure a Service or Application…’
3- In the High Availability Wizard, click next on the first page, then select ‘Virtual Machine’ from the list of available service and application types.
4- Select the virtual machines you wish to make highly available and follow the wizard to completion.