According to VS's web site, they only use the A340-600 on the VS200/ VS201 to HKG/ SYD. It still looks to me that these a/c are going to MNL and back empty. That is really environmentally friendly but of course this will not be mentioned on their web site.
I would imagine if there are an empty ferry flights they would be HKG to MNL and return. An aircraft comes off a check and is ferried to HKG. The aircraft which is due a check does the service to HKG, and is then ferried to MNL. The aircraft which came off the check then does the service to SYD. Sound feasible?