Residual Hyper-V checkpoints remaining after differential disk (.avhdx) merge

From this article, you will learn how to resolve an issue where checkpoints remain in Hyper-V Manager after differential disk (.avhdx) files have been merged, and cannot be removed.

After merging differential disks (.avhdx) of a Hyper-V virtual machine, residual checkpoints may remain visible in Hyper-V Manager. These checkpoints cannot be removed either through the graphical interface or using PowerShell commands.

Issue

Residual virtual machine checkpoints persist in Hyper-V Manager and cannot be deleted via standard management tools such as Hyper-V Manager or PowerShell.

Cause

This situation may occur, for example, when manual merging of differential disks is performed through PowerShell commands while Hyper-V Manager remains open. In such a case, .avhdx files are correctly merged into the base .vhdx file; however, the checkpoint metadata is not removed. There may be additional scenarios leading to the same state, but this one is among the most common.

Resolution

1. Verify disk merge completion Before attempting manual checkpoint removal, ensure that incremental (.avhdx) disks have been successfully merged into the main virtual disk. In the VM’s settings, verify that the virtual hard disk path points to a .vhdx file, not an .avhdx.

2. Shut down the virtual machine For the integrity of the operation, power off the virtual machine before making any changes.

3. List existing checkpoints Open PowerShell as Administrator and run:

Get-VMSnapshot -VMName [VirtualMachineName] | Select-Object Name, Id

Replace [VirtualMachineName] with the actual name of the virtual machine as displayed in Hyper-V Manager. This command will return the names and IDs of all snapshots associated with the VM.

For more detailed information, execute:

Get-VMSnapshot -VMName [VirtualMachineName] | Format-List

1. Locate snapshot files In the VM settings, identify the path where snapshots are stored, and navigate to this directory in File Explorer. You will find folders and files named according to the snapshot identifiers returned earlier. Do not delete them yet, as they are still locked by the Hyper-V service. Hyper-V Manager > Settings > Checkpoints > Checkpoint file location

2. Stop the Hyper-V Virtual Machine Management Service Open the Services console (services.msc) and stop the service named "Hyper-V Virtual Machine Management service" (VMMS). Alternatively, from PowerShell:

Stop-Service vmms

1. Delete orphaned snapshot folders Once the service is stopped, delete all folders and files corresponding to the problematic snapshot identifiers.

2. Restart the management service Restart the previously stopped service:

Start-Service vmms

1. Verify in Hyper-V Manager Reopen Hyper-V Manager and confirm that the previously persistent checkpoints no longer appear in the list of snapshots.

Summary

Residual checkpoints after .avhdx consolidation are typically caused by metadata desynchronization between disk files and Hyper-V’s configuration. The outlined procedure safely removes orphaned checkpoint references while preserving the integrity of the merged virtual disks.