This issue can occur if a vRealize Automation managed virtual machine requires to be restored from backup.
Resolution
Find the original value of the instance UUID. In the database, look at the dbo.VirtualMachine table and find the missing machine. You can use this SQL statement to narrow down the options:
SELECT * FROM [vCAC].[dbo].[VirtualMachine] WHERE [IsMissing] = 1
Power off the machine in vCenter
Unregister the VM -- IMPORTANT!!!
Use "Remove from inventory" -- do not delete the machine and its virtual disk
Edit the .vmx file. Find the line that contains the vc.uuid, and replace it with the value from step 1.
If you cannot get on an ESX host (using SSH), then you will need to download the file and upload it after it is changed, using the datastore browser.
Register the VM by going to the datastore browser, clicking on the vmx file and choosing "Register VM..."
Power on the virtual machine.
Force a data collection in vRealize Automation.
Review the status in vRealize Automation.
The machine should now have status other than "Missing" in the vRA inventory.
Additional Information
If there are a large number of systems impacted, open a Service Request with Global Support Services with this Knowledge article in reference requesting assistance restoring these virtual machines.