Did you ever get a resolution to your error? I'm having the same problem. Pool seems to function properly besides the error
I know this is an old thread, but I just found a work-around at least for our situation. We're still on 5.1.3 (on our way to phasing out linked clones), and I started encountering this error during summer refresh time last year (K-8 school). Odd thing is that not all VMs were throwing this error, even within the same pool. I couldn't narrow it down to VMs being on a specific data store.
I tried the troubleshooting step suggested at Unable to recompose desktop, Unable to resync VM - Could not find VC object op type VirtualMachine, and id (recreating a fresh snapshot of the parent VM while provisioning is disabled on the pool), but that just eliminated the parent VM/snapshot as a source of the issue.
Since the pools currently active are for faculty and staff, we have persistent disks in place. My fix, via the VMWare View Console was to detach the persistent disks, which removed the associated VM, then rebuild the individual VMs from their detached persistent disk.
Hope that's helpful to someone.