After the HyperV discovery if the VMs are missing, query the below table and check
select * from hyperventitymomap where entity_type = 'HyperV-VM';
select * from hyperventitymomap where entity_type = 'HyperV-Host';
When the MOID is -4, check whether their DNS resolves, if not update it from hyperv server manager
When the MOID is -5, that's marked as "deleted by user" so opmanager won't be mapping it.
We have run this update query manually and restart opmanager service.
update hyperventitymomap set moid = -4 where moid = -5;
Now automatic discovery will initiate during every restart.