I'm trying to enable Change Block Tracking as per this VMWare KB article but the setting ctkEnabled is not being retained in the advanced options or being added to the vmx file.
The setting scsi0:0.ctkEnabled is being retained and I see a file vmname-ctk.vmdk in the datastore.
I've verified that the vm doesn't have any snapshots but don't see any other suggestions in the KB (or google, of course.)
Edit:
The last comment on this community post. It's a slightly different circumstance, but suggests that there is an known bug editing these settings in the web-gui.
Have you checked the prerequisites here?
Also, can you explain at which stage the setting disappears, e.g.: immediately after configuring, Etc.?
One VM doesn't work, but many others do? This is really a troubleshooting exercise that we may not be able to help you with... Granted, I've never needed to do this as VMware's vSphere Data Protection adds this to the virtual machine configuration automatically.
You could just add the requisite lines to the offending VM's configuration file manually.
Things that help to know in general: