Virtual Machine Snapshot Consolidation fails with error "An error occurred while deleting a snapshot: One of the disks in this virtual machine is already in use by a virtual machine or by a snapshot."

Products

• VMware vCenter Server

Issue/Introduction

• In the UI, when editing Virtual Machine settings, we can see the Virtual Machine is not using the snapshot vmdk but the expected base disk.
• In the vmware.log of affected Virtual Machine we see similar errors to below: 

2025-06-04T#########Z Er(02) vmx ############# SNAPSHOT: SnapshotGenerateDeleteDisks Failed to fetch disk tree: One of the disks in this virtual machine is already in use by a virtual machine or by
a snapshot (21)
2025-06-04T#########Z Er(02) vmx ############# SNAPSHOT: SnapshotDeleteNode failed: One of the disks in this virtual machine is already in use by a virtual machine or by a snapshot (21)
2025-06-04T#########Z Er(02) vmx #############  SNAPSHOT: Snapshot_Delete failed: One of the disks in this virtual machine is already in use by a virtual machine or by a snapshot (21)
2025-06-04T#########Z In(05) vmx ############# VigorTransport_ServerSendResponse opID= #############   seq= #############  : Completed Snapshot.Delete request with messages in 5599 US.
2025-06-04T#########Z In(05) vmx - VigorTransportProcessClientPayload: opID= #############   seq= #############  : Receiving Snapshot.Delete request.
2025-06-04T#########Z In(05) vmx #############  DISKLIB-VMFS  : "/vmfs/volumes/ #############  /Example-VM/Example-VM-flat.vmdk" : open successful (5) size = 96636764160, hd = 0. Type 3
2025-06-04T#########Z In(05) vmx #############  DISKLIB-VMFS  : "/vmfs/volumes/ #############  /Example-VM/Example-VM-flat.vmdk" : closed.
2025-06-04T#########Z In(05) vmx #############  SNAPSHOT: SnapshotDiskTreeAddFromSnapshot: Trying to add snapshot Example-VM-Snapshot.vmsn to disk/vmfs/volumes/ #############  /Example-VM/Example-VM.vmdk which already has snapshot currentState.
2025-06-04T#########Z Er(02) vmx  #############  SNAPSHOT: SnapshotGenerateDeleteDisks Failed to fetch disk tree: One of the disks in this virtual machine is already in use by a virtual machine or by
a snapshot (21)
2025-06-04T##########Z Er(02) vmx #############   SNAPSHOT: SnapshotDeleteNode failed: One of the disks in this virtual machine is already in use by a virtual machine or by a snapshot (21)
2025-06-04T#########Z Er(02) vmx  #############   SNAPSHOT: Snapshot_Delete failed:One of the disks in this virtual machine is already in use by a virtual machine or by a snapshot (21)

• In the vmware.log of the Virtual Machine, you may see events for VM guest OS being powered off and after the power back on task snapshot consolidation fails (this is one example of identifying if any changes were made around time issue occurred)

Example: 

2025-06-04T######### In(05) svga - MKSScreenShotMgr: Taking a screenshot
2025-06-04T#########In(05) vcpu-3 - PCIXHCI: Interrupt type changed from MSIX to INTX
2025-06-04T######### In(05) vcpu-0 - PIIX4: PM Soft Off.  Good-bye.
2025-06-04T#########In(05) vcpu-0 - Chipset: The guest has requested that the virtual machine be powered off.
2025-06-04T#########No(00) vcpu-0 - ConfigDB: Setting softPowerOff = "TRUE"

• CBT may be enabled on the Virtual Machine for incremental backups 

Environment

vCenter Server 8.0 

ESXi 8.0 

Cause

Due to a reconfigure task implemented during a snapshot task initiated by a backup solution, the snapshot chain was altered and broken causing consolidation to fail

Resolution

Please review following article on best practices on snapshot commitment and consolidation and steps under Additional Information to assist with resolving the issue:  Consolidating/Committing snapshots in VMware ESXi