Issue:
The following error is reported when you attempt to change the datastore used by the virtual machine using the vCenter Migration Wizard in vCenter Server 4.1. This process is typically called Storage vMotion.
A general system error occurred: The virtual machine has virtual disk in link-cloned mode that prevents migration.

Cause:
The VM most likely has un-committed snapshots not listed in the SnapShot Manager.
Solution:
Use the following procedure to have vCenter Server / ESX properly show the Snapshots on the virtual machine and commit them to the Base VMDK file.
1) Edit VM Settings
a. Review path of hard drive VDK file

b. Note if this is the Base VMDK for or a Snapshot VMDK file.
i. Base VMDK files are the filename.vmdk and filename_#.vmdk file.
ii. Snapshot VMDK files are the filename-######.vmdk files.
c. Note which LUN Hard disk 1 resides on, this will contain the VMX file.
d. Perform all the following steps.
2) Power Off VM
3) Remove the VM from the vCenter Inventory
4) Add the VM to vCenter Inventory
a. Right click the VMX file and Select Add to Inventory
5) Using Snapshot Manager for this VM
a. If any snapshots appear, select the top snapshot
b. Click Delete All
i. This will commit them to the base vmdk
6) Create a test snapshot
a. Don’t quiesce the OS
b. Wait for it to complete
7) Using the Snap Manager for this VM
a. Select the current snapshot
b. Click Delete All
8) Edit VM Settings
a. Review path of hard drive VMDK file
b. This should now be the base VMDK file
9) Power on the VM
10) Browse the datastore and folder where the VM resides
a. Sort by file type
b. Look for the Snapshot file type

i. Select these file and delete them
ii. Optional: check the dates of the file to see how recent they are.
c. Look for the Virtual Disk type

i. Select the -######.vmdk files and delete them
ii. These are the VMDK files of the snapshots
iii. Keep the Base VMDK files listed in VM Settings you reviewed earlier.
iv. Optional: check the dates of the file to see how recent they are.
d. Note: Since the VM is powered on, the VMDK files cannot be deleted if they are in use by the VM.
11) You can now Storage vMotion the VM.
a. If you fail to delete the Snapshot VMDK files, they will be left on the original LUN until manually deleted.
More Information:
You can use this command to file all VM’s (their paths) that have Snapshots (aka: delta files).
find /vmfs/volumes -name "*-delta.vmdk"
Committing snapshots when there are no snapshot entries in the snapshot manager
Storage vMotion fails with the error: virtual machine has virtual disk in link-clone mode