1. Reset CBT using any of the previously posted methods; manually with reboot or script with snapshot method (both work). Then just browse the data files and confirm that the <diskname>-ctk.vmdk files are gone. This should be enough, but if you want to really really make sure, also to the next step.
2. Let Veeam run a backup job on the VM after the reset and look for the following in the Veeam logs (%programdata%\Veeam\Backup\VMNAME\Task.VMNAME.vm-nnn.log):
[04.11.2014 06:30:17] <60> Info VM information: name "VM NAME", ref "vm-nnn", uuid "564d6345-3311-21da-9f59-a7188eb2062e", host "vsphere.hostname.local", resourcePool "resgroup-73", connectionState "Connected", powerState "PoweredOn", template "False", changeTracking "False", configVersion "vmx-07"
As you see veeam reports changeTracking as "False"
You can then some lines below find:
[04.11.2014 06:30:25] <60> Info [Soap] SetVmChangeTracking, vmRef 'vm-nnn', changeTrackingEnabled 'True'
[04.11.2014 06:30:25] <60> Info [VimApi] ReconfigVM, type "VirtualMachine", ref "vm-nnn"
So, veeam is trurning CBT back on
That's all folks

Brgs,
Kim Alexander Hansen