How to Recover VMware | Hyper-V Virtual Machines After Snapshot Corruption [2025 Guide]

You power on your critical SQL server or Domain Controller, only for it to fail. And the error message is cryptic, something like: “The chain of virtual hard disks is corrupted” or “Parent virtual disk has been modified.”

If you’re a database admin, you’ll know that few things are as terrifying as a broken snapshot chain. Whether you run VMware ESXi or Microsoft Hyper-V, snapshot corruption means that your virtual machine (VM) has lost track of the timeline between its base disk and its current state.

You can recover VMware snapshots, but you’ll require surgical precision. One wrong move with a command-line tool and you might permanently sever the link, leaving you with terabytes of inaccessible data. This guide will detail technical steps to repair VMDK and AVHDX snapshot chains using native tools and explain when it’s better to contact VM data recovery professionals like Stellar.

Understanding Snapshot Corruption: The “Chain of Trust”

Snapshots are differencing disks, not backups. When you take a snapshot, the hypervisor freezes the base disk (parent) and writes changes to a new delta disk (child). This creates a rigid dependency. The child disk holds only new data blocks; the parent holds the original.

If this link breaks (perhaps the parent ID changes or a merge fails), the child becomes an “orphan.” It still has the data but lacks the map to place it. Since the child relies on sector offsets relative to the parent, any modification to the parent points those offsets to the wrong data, corrupting the guest OS file system.

Snapshot Architecture: VMware vs. Hyper-V

Diagnosing the failure starts with identifying the specific files involved. In our experience, confusing these formats is what leads to disastrous “fixes.” So let’s understand them.

Feature	VMware vSphere	Microsoft Hyper-V
Descriptor File	.vmdk (Text file)	Embedded in Binary Header
Data File	-flat.vmdk (Base) / -delta.vmdk (Snap)	.vhdx (Base) / .avhdx (Snap)
Tracking ID	CID (Content ID) & ParentCID	Internal GUID & ParentGUID
Common Error	CID mismatch detected	Chain of virtual hard disks is corrupted
Merge Tool	vmkfstools / vSphere Client	PowerShell Merge-VHD / Hyper-V Manager

Why Does a Snapshot Chain Break?

Corruption usually stems from interrupted processes or storage management errors. These include the following.

⚡ Interrupted Merges

Host server crashes or power loss during consolidation (merging Child into Parent) can mismatch header data. The hypervisor may mark the merge as complete before data blocks move.

💾 Parent Modification

Powering on or modifying a parent disk changes its CID. Child snapshots fail immediately because their “ParentCID” check no longer matches the base.

🚫 Storage I/O Errors

Bad sectors on physical SANs or SSDs prevent the hypervisor from reading link metadata, breaking the chain even if files remain intact.

🔒 LUN Locking

Backup solutions (e.g., Veeam, Datto) sometimes lock a file and fail to release it. This leaves a “phantom” snapshot that the hypervisor thinks is active, preventing consolidation.

Method 1: Repairing Your VMware Snapshot Chains (VMDK)

In VMware ESXi, CID mismatch is the most frequent culprit. The child disk expects a specific ParentCID from the base disk. If the base disk was touched, the link breaks.

Step 1: Diagnose the Mismatch

Confirm the mismatch before editing.

1. Enable SSH on your ESXi host; connect via PuTTY.
2. Navigate to the VM folder: cd /vmfs/volumes/DatastoreName/VMName.
3. Check log. Look for: DiskLib_Open: CID mismatch detected. The parent CID of the child disk does not match the CID of the parent disk.

Step 2: Edit the Descriptor File

Manually edit the descriptor file (the small text .vmdk file, never the large -flat.vmdk).

1. Get the parent’s CID: cat parent.vmdk | grep CID. Note the 8-digit hex code.
2. Open the child descriptor: vi child-00001.vmdk.
3. Find parentCID=xxxxxxxx. It likely won’t match the value from step 1.
4. Update the value to match the parent’s current CID.
5. Save and exit (:wq).

Warning: Back up descriptor files first. One typo can render the entire disk unreadable.

Step 3: Consolidate With vmkfstools

If the chain is valid but the UI is confused, force a clone. This reads the snapshot chain and writes a new, single flat VMDK.

1. Run: vmkfstools -i child-00001.vmdk recovered_vm.vmdk
2. This merges the child state with all parents into a fresh file.
3. If successful, attach vmdk to a new VM to access data.

Method 2: Fixing Hyper-V AVHDX Chain Issues

Hyper-V snapshot chains (AVHDX) use binary headers, so you cannot edit them in text editors. PowerShell is your primary friend here.

Step 1: Identify the Chain

You can inspect the disk relationship to ensure every child points to a valid parent. To do this, open PowerShell and input the following command:

Get-VHD -Path “D:\VMs\Disk_UUID.avhdx” | Select Path, ParentPath, VHDType

If ParentPath shows a missing or mismatched file, the chain is broken. This Microsoft forum post troubleshoots this problem in more detail, if you’re struggling with snapshot and checkpoint issues.

Step 2: Manually Merge the Chain

Next, if Hyper-V Manager fails, you must force a merge via PowerShell. Merge from the newest child back to the oldest parent. Here’s how to carry this out.

1. First, ensure the VM is off.
2. Run: Merge-VHD -Path “C:\VMs\Child.avhdx” -DestinationPath “C:\VMs\Parent.vhdx”
3. Warning: Use -IgnoreIdMismatch only as a last resort. If data blocks don’t align, you will corrupt the guest file system.

Step 3: The Export/Import Fix

For “orphaned” checkpoints, export the VM.

1. To Export: Right-click the VM in Hyper-V Manager, and select Export.
2. To Import: Delete the old VM from inventory (keep disk files). Select Import Virtual Machine, point to the export, and choose Register the virtual machine in-place.
3. This clears any “phantom” checkpoint references blocking backups or booting.

When Native Tools Fail and the Risk of Data Loss

vmkfstools or Merge-VHD often fail if the AVHDX/VMDK internal structure is damaged. This could be due to Bit Rot or Header Corruption. If the hypervisor cannot parse the header, it cannot merge. You might be tempted to try these, but be wary, as they can complicate VM recovery efforts.

⚠️ The CHKDSK Trap

Don’t mount a broken snapshot chain on the host to run CHKDSK. Windows can see missing parent data as “bad index entries” and will try fixing them by deleting the index. You might mount the drive, but your database tables will be gone.

⚠️ Avoid “Force” Flags

Forcing a merge on mismatched disks (-IgnoreIdMismatch) can result in a VM that boots but contains corrupted databases or unreadable files. If native hypervisor tools cannot read the disk, the corruption is likely at the binary level.

How Stellar Can Help With VMware Snapshot Corruption

When native Hyper-V VM recovery fails, you need a solution deeper than the hypervisor. Stellar’s VM data recovery service specializes in reconstructing broken virtual environments.

Stellar’s in-lab experts in India analyze raw hex data of corrupted snapshot files. Instead of trying to “fix” the Hyper-V snapshot in-place (which risks data alteration), we virtually reconstruct the file system. We map data blocks from child to parent using proprietary algorithms that bypass broken hypervisor links. With Stellar, you get:

✅ Proprietary Tools: Custom algorithms for AVHDX/VMDK structure repair.

✅ ISO-Certified Security: Data handled in ISO 9001- and ISO 27001-certified centers, ensuring privacy and process quality.

✅ Class 100 Cleanroom Lab: If failure stems from hardware issues (RAID controller crash, SSD firmware panic), recovery is done in a contaminant-free environment.

If your snapshot chain breaks and production halts, don’t gamble with CHKDSK. Stellar recovers critical data from all major VM platforms, including VMware vSphere, Microsoft Hyper-V, Oracle VirtualBox, Citrix XenServer, Virtual Desktop, and more. Contact Stellar Data Recovery service today for a free consultation.

Preventive Tips to Avoid Snapshot Failures

If you want to avoid the headache of failing snapshots and corrupted VMware altogether, follow these industry-standard best practices.

🌡️ Monitor Storage Health

Watch for I/O timeouts that precede corruption. This is an easy warning sign to catch early.

🔄 Keep Chains Short

Consolidate your snapshots within 72 hours. The longer the chains, the greater the merge corruption risk.

⚡ Use VSS-Aware Backups

Use dedicated backup software (like Veeam/Altaro) that triggers VSS for database consistency.

🔌 Never Modify Files Manually

Don’t rename, move, or edit AVHDX/VMDK files while the VM runs. All these actions can cause corruption by changing the state.

FAQs

1. Can I manually delete .AVHDX files to save space?

No. Deleting an AVHDX file destroys the VM’s “future” data. You must merge them into the parent disk using Hyper-V Manager or PowerShell.

2. What does "CID mismatch" mean in VMware?

It means the child snapshot expects the parent disk to have a specific ID signature. If the parent was modified independently, its ID changes, and the child can no longer link to it.

3. Is it safe to use text editors on VMDK files?

Text editors should only be used on small descriptor.vmdk files (a few KB). Never open large -flat.vmdk (data) files in a text editor; it corrupts binary data.