Are you saying the vmx file is missing since a VM powered down but then shutdown event was seperate from the HA failover? I assume this VM is using shared storage?
Why/When VM Powered Down: VMware Knowledge Base
neither contain information about the vmhost, they are VM specific files
HA is independant* of vCenter, the hosts use heartbeats to determine when a host has failed or become partitioned. See the following
*vCenter can be involved when DRS is required to free up slots on hosts when using admission control etc. Overall though, HA will work even when vCenter is offline