Production Checkpoints on 2k8/2k8R2 Domain Controllers - Not supported.
See this kb https://technet.microsoft.com/en-us/library/dn818483(v=ws.11).aspx
Production Checkpoint of a machine running Edge Transport role (ADAM VSS writer). Not supported.
This is directly from MSoft Premier support.“Microsoft does not support the use of checkpoints on virtual machines running the Active Directory Domain Services role (also known as “domain controllers”) or the Active Directory Lightweight Directory Services role in Windows Server 2008 or Windows Server 2008 R2. For more information, see Operational Considerations for Virtualized Domain Controllers (http://go.microsoft.com/fwlink/?LinkId=159631).”
*ADAM is former name of AD LDS.
Exchange 2010 backups on hyper-v 2016 with AAP enabled. Works. (As long at edge transport role is not installed) This above would also explain why virtualised SBS etc doesn't work on a 2016 host.
Not sure about production checkpoints on AD 2012 or Exchange 2013 (I imagine exchange 2013 is same as above). I understand Veeam is still investigating/clarifying with Microsoft exactly what is/isnt supported in relation to AD checkpoints.
Many thanks to Rustam and Veeam support team for their assistance in getting some answers on this.