Problem
When a virtual machine has been removed, for example by using Hyper-V Manager or Cluster Administrator, it remains visible in the SCVMM Console.
When youright-click on the VM, the options “Delete” or “Repair” do not work.

Cause
Haven’t got a clue… Sounds like some sort of bug?

Resolution
Yes, you can do it in a GUI… just look up the *.xml file for the virtual machine and delete it.
However, I prefer to use the SCVMM PowerShell module:

Get-VMMServer -ComputerName “SCVMM”
$VM = Get-VM -Name “VirtualMachineName”
Remove-VM -VM $VM -Force