vSAN VM consolidation fails with "Inappropriate ioctl for device" and "File was not found" due to missing base vSAN object

Products

• VMware vSphere ESXi
• VMware vSphere ESXi 8.0

Issue/Introduction

• Virtual machine triggers a "Virtual machine disks consolidation is needed" alarm.
• Manual consolidation tasks fail with: "File was not found" or "The system cannot find the file specified."
• Snapshot creation/deletion fails with similar file-not-found errors.
• VM power-on attempts fail with "Unable to enumerate all disks."
• Entries similar to the following are seen in the /var/log/vmkernel.log:
  
  Vol3: Unable to register file system [UUID] for quiesce timeout notifications: Inappropriate ioctl for device

Unmap6: could not obtain partitionInfo for device [ID]: Inappropriate ioctl for device

Environment

VMware vSphere ESXi 8.x

Cause

• This issue occurs if the underlying vSAN data payload (the base object) for a virtual disk has been destroyed or permanently deleted from the vSAN datastore.
• This results in a broken snapshot descriptor chain. Because the physical data block for the base disk is absent, the snapshot descriptor attempts to reference a parent extent that no longer exists on the storage fabric.

Resolution

Because the physical vSAN data object is destroyed, reconstruction of the text descriptors is impossible. The only structurally sound method to recover the data and clear the consolidation failure is a restoration from backup.

1. Verify the missing object:
   • Identify the snapshot descriptor in the VM directory (e.g., VMNAME_1-000001.vmdk).
   • Run vmkfstools -q -v10 [snapshot_vmdk_path] to check for a missing parent extent.
   • Use esxcli vsan debug object list | grep -B2 -A5 "VMNAME" to confirm if the base vSAN data object UUID is missing from the storage fabric.
2. Unregister the VM: Remove the orphaned VM configuration from the vCenter inventory to clear stale database entries.
3. Restore from backup: Restore the VM from a known-good backup repository to recover the missing physical data payload and rebuild a healthy snapshot chain.

Additional Information

Related KB:

"An error occurred while consolidating disks" when deleting one or more snapshots or consolidate disks