Hi Jeff,
Since you are pro at this now, and also because it's just the boot drive, you probably don't need the rescue folder. You can just shutdown the guest, make a backup of the vmx, perform your clone of the boot drive to the same or another directory, then remove the boot disk (Edit Settings) that was pointing to the current snapshot. Say ok, then add the newly cloned disk. Power up. Clean up old files once happy (and of course only if the machine is powered up as files in use cannot be deleted).