OK so here is a tricky problem with an easy fix.
Sometimes, in SC VMM 2012 some of my VMs are shown as “missing”. I cannot do anything to them using VMM. An easy fix is to fire up FCM (Failover Cluster Manager) and live migrate or quick migrate the VM (depending upon whether the VM is running or not). After that VMM will immediately refresh the VMs state to the correct one….stopped or running.