If you go back to the same VASS person before it expires surely they would be able to cut you a deal on updating the cert.
But it does beg the question of what happens when you want to sell the car - do you have to get a new VASS inspection done? I understand with RWC you need a fresh one each time the car changes hands, but VASS certs are 5 to 10 times the cost and it doesn't seem reasonable to have to spend that over and over. Plus what's the point of a mod sticker/plate if you have to keep getting the car re-certified?
With your situation, I'd be tempted to just front up at VicRoads and play dumb - the last time I went in the lady behind the desk would have been quite happy to process my paperwork without any VASS cert at all...