You can't delete a recovery checkpoint for a virtual machine in Data Protection Manager
This article describes an issue that blocks you from deleting a broken recovery checkpoint for a virtual machine in System Center 2012 Data Protection Manager.
Applies to: Windows Server 2012 R2
Original KB number: 3059372
After Data Protection Manager (DPM) backup fails, you can't delete broken recovery checkpoints for a virtual machine that was created by Hyper-V. When you try to do this, you discover that there's no option listed for a virtual machine in the Hyper-V Manager Console GUI.
The following command returns the list of snapshots for the VM and its type:
Get-VMSnapshot -VMName <virtual machine name>
The snapshots that Hyper-V typically creates are of the Standard type. However, DPM creates snapshots of the Recovery type. In the list that's returned, you have to delete the Recovery snapshots, as these are actually the broken checkpoints.
How does DPM work?
Generally, DPM requests Hyper-V to create a checkpoint for the virtual machine as part of the VM backup process. After DPM completes the backup, it sends a backup complete notice, and then Hyper-V merges the checkpoint back into the primary .vhd file and deletes the .avhd file.
What causes broken checkpoints?
There's a known issue in which Windows Server leaves a virtual machine in a locked or backup state even after backup is complete. To resolve this issue, apply the hotfix that's described in Hyper-V virtual machine backup leaves the VM in a locked state.
However, even after you do this, the broken recovery checkpoints remain.
There's no way to delete the broken recovery checkpoints through the GUI. Instead, you must manually merge them. For information about how to merge the .avhd files into the .vhd file, see Manually merge .avhd to .vhd in Hyper-V.
This resource also suggests that a better solution (if you have 2008 R2 or later) is to create a snapshot of the VM. Then, select that snapshot and export it. This creates a copy of your VM in a single VHD file. You can then remove the old VM and import the new one.