There are two workarounds available:
Add the cloud.uuid parameter to each linked clone to cause Snapshot Hunter to not attempt to process that VM.
The cloud.uuid parameter will need to be added to each affected VM. If vCloud Director is not being used, the content of the cloud.uuid parameter does not matter. Snapshot Hunter only checks the VMX to see whether or not the parameter exists. You can add the parameter to a VM using a vSphere client, a PowerCLI script, or by editing the VMX file using the editor available in Veeam B&R’s Files view.
Disable Snapshot Hunter entirely.
Snapshot Hunter can be disabled which will disable automatic consolidation for all VMs. Warnings regarding VMs that Backup and Replication believes need consolidation will still occur.
Create the following registry value on the backup server:
Key: HKEY_LOCAL_MACHINE\SOFTWARE\Veeam\Veeam Backup and Replication
Value name: DisableAutoSnapshotConsolidation
Value type: DWORD
Value: 1 = disable consolidation, 0 = enable consolidation
To apply the changes made in the registry the Veeam Backup Service must be restarted. Ensure that all jobs are stopped before doing so, when the service stops it will terminate all running jobs.