This article provides the workaround when the managed VMs gets deleted/shows missing from vRA
The issue was happening during data collection (enumeration) of VMs. If a VM is being provisioned at the same time data collection is running, in some instances, the data collection processing can delete this machine from vRA. The machine does not get deleted from vCenter.
Recommend to follow the workaround for now.
The issue is addressed in versions from 8.2 P2 onwards.
The missing machines will need to be onboarded in vRA. The missing machines can be onboarded into a single project or in separate projects. The onboarded machines can then be added to the relevant deployment.
Here is the documentation for the Onboarding plans in vRealize Automation Cloud Assembly