Orphaned checkpoint on a VM with no "delete" option

Takami Chiro 311 Reputation points
2026-09-02T19:47:05.0966667+00:00

Hi everyone,

Hope you are all doing well~~

I got into an issue with one of the VM in Hyper-V. There were 6 Orphaned checkpoint created unexpectedly (not manually created for sure). I think those were caused by the backup system (__bric) and now backup fails on it it now. I tried to remove the orphaned checkpoint like what I did to the other checkpoints in the past. However, I could not find the "delete" option in the menu.

I am doing an export of it as a backup now.

In the web, I found this command, "Get-VMSnapshot -VMName "vmname" | Remove-VMCheckpoint". I would like to ask:

1.) Is this safe to run without corrupting the vm itself?

2,) Also, will it remove all checkpoints of that vm (in my case is 6)?

3.) Would this command automatically merge with the primary copy first (so the vm stays with all the updates) before the checkpoint is removed?

Also, another question I have is:

I have a replication running for this VM between two hosts (not a cluster). If I do a planned failover for the VM to the replica host and make the replica to become the primary live. Then reset the replication by deleting the existing replication relationship. Would that get rid of the orphaned check point too? Any risk by doing this?

Hope you can help. Thank you for your help in advance.

Takami Chiro

Windows for business | Windows Server | Storage high availability | Virtualization and Hyper-V
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Answer accepted by question author
Daphne Huynh (WICLOUD CORPORATION) 1,385 Reputation points Microsoft External Staff Moderator
2026-09-03T07:25:46.8066667+00:00

Welcome to Microsoft Q&A,

Thank you for taking the time to provide these details. It's a good step that you're creating an export as a precaution before making any changes.

In general, do not manually delete AVHDX or checkpoint files from disk. If the checkpoints are still visible to Hyper-V, using PowerShell is the supported approach.

The following command: Get-VMSnapshot -VMName "VMName" | Remove-VMSnapshot (or Remove-VMCheckpoint on newer versions of Hyper-V) is a supported Hyper-V cmdlet that removes checkpoints through Hyper-V and initiates the required merge process. Deleting a checkpoint does not discard the VM's current state. Instead, Hyper-V merges the associated AVHDX files back into the parent virtual disk while preserving the latest data and changes.

  • Regarding your questions:

1. Is it safe to run?

Generally, yes. As long as the checkpoint chain is healthy and you have a valid backup or export available, this is the supported method for checkpoint removal. The cmdlet does not directly delete the VM's virtual disk.

2. Will it remove all 6 checkpoints?

Yes. Since Get-VMSnapshot returns all checkpoints for the specified VM and passes them to Remove-VMSnapshot, all six checkpoints would be processed for removal.

3. Will it merge the changes before removing them?

Yes. Hyper-V merges the checkpoint data into the parent disk as part of the checkpoint removal process, ensuring the VM retains all updates and changes contained within the checkpoint chain. Depending on the size of the checkpoints and storage performance, the merge operation may take some time to complete.

  • Regarding Hyper-V Replica

A planned failover to the replica host followed by deleting and recreating the replication relationship is not typically recommended as a method for removing orphaned checkpoints. While rebuilding the replication relationship may create a new replication chain, it does not guarantee that orphaned checkpoint metadata or AVHDX files will be cleaned up. It also introduces additional complexity and risk compared to addressing the checkpoint issue directly.

Since the checkpoints may have been created by a backup application, I would recommend the following before proceeding:

  1. Verify that no backup jobs are currently running.
  2. Check whether the backup software has left behind any recovery or backup-related checkpoints.
  3. Complete the VM export or ensure you have a recent backup.
  4. Use Get-VMSnapshot to confirm which checkpoints Hyper-V currently recognizes.
  5. Remove the checkpoints using the supported Hyper-V cmdlets.

If these checkpoints are truly orphaned and do not behave like normal Hyper-V checkpoints, additional investigation of the AVHDX chain and the backup application's logs may be required before attempting any manual repair actions.

As the backup jobs are already failing on this VM, I would strongly recommend confirming that your export or backup is valid before removing the checkpoints. Backup-generated recovery checkpoints can occasionally become orphaned if a backup operation was interrupted or did not complete successfully.

Reference: Remove-VMSnapshot (Hyper-V) | Microsoft Learn

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  1. AI answer

    2026-09-02T19:47:25.74+00:00

    For orphaned or backup-created Hyper-V checkpoints, the supported guidance is:

    1. Do not delete .avhdx files directly. That can break the virtual disk chain.
    2. If the checkpoint is visible but the GUI has no usable delete option, PowerShell is the next supported path.

    For the command:

    Get-VMSnapshot -VMName "<VMName>" | Remove-VMSnapshot
    • It is the documented PowerShell method when checkpoints are visible but can’t be deleted in Hyper-V Manager.
    • It removes the checkpoints returned by Get-VMSnapshot for that VM, so if 6 checkpoints are returned in the pipeline, all 6 are targeted.
    • Hyper-V checkpoint deletion merges the .avhdx data back into the parent .vhdx/disk chain; the .avhdx file is deleted after the merge completes.

    For backup-created checkpoints specifically:

    • Get-VMSnapshot -VMName <virtual machine name> can show the snapshot type.
    • Hyper-V normally creates Standard snapshots, while Data Protection Manager creates Recovery snapshots.
    • If the orphaned items are backup-created recovery checkpoints, identify those in the output and remove those recovery snapshots.

    Recommended sequence:

    1. Run: 
         Get-VMSnapshot -VMName "<VMName>"
      Confirm what checkpoints exist.
    2. If they are visible there, remove them with: 
         Get-VMSnapshot -VMName "<VMName>" | Remove-VMSnapshot
    3. If deletion does not succeed, shut down the VM and retry. Shutdown can trigger an auto-merge if possible.
    4. If merge still fails, use Hyper-V Manager > Edit Disk > select the .avhdx > Merge > To parent virtual disk.

    Risk note: before merges, deletions, or major configuration changes, back up critical VMs. Also, removing checkpoints can cause loss of unsaved or transient data.

    About whether the VM keeps its updates: yes, checkpoint deletion is designed to preserve the current state by merging the differencing disk data back into the parent chain rather than discarding it.

    About planned failover / breaking and recreating replication: no guidance in the available documentation states that planned failover or resetting Hyper-V replication will remove orphaned checkpoints, so that should not be treated as the supported fix here.

    If the checkpoints are not visible in Hyper-V Manager or deletion still fails, inspect the disk chain and orphaned AVHDX files:

    Get-VMHardDiskDrive -VMName <VMName> | ForEach-Object { Get-VHD -Path $_.Path | Select-Object Path, ParentPath, VHDType }

    Then merge orphaned .avhdx files manually if needed:

    Merge-VHD -Path <path-to-avhdx> -DestinationPath <parent-vhdx>

    References:

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