After fighting this issue for months, I have found a 'solution' that works. The behavior we were experiencing is that Veeam would only work for two days in a row. After the second day, Hyper-V would fail to merge the snapshot. We had to shutdown the VMs and then restart the VMMS service to get a successful merge (and therefore a successful backup).
From this site: https://social.technet.microsoft.com/Fo ... rverhyperv
I removed the GPO: User rights assignment/Log on as a Service, followed by a GPUpdate / Force on the Hyper-V machine. The stopped all VM's, rebooted the server - and the problem did not surface again.
Instead of just disabling this, you could also just add the proper user needed by Hyper-V to the logon as a service GPO. However, I am not sure what it is. 'Virtual Machines' alone doesn't solve this issue.
Hope this helps someone!