Wirelessly posted (BlackBerry: BlackBerry8530/5.0.0.1030 Profile/MIDP-2.1 Configuration/CLDC-1.1 VendorID/417)
The combo ticket is one card: the LIRR ticket on one side, and the Metrocard (with a magnetic strip) on the other side. I was not able to refill the Metrocard portion of my LIRR combo ticket after the LIRR conducted punched the ticket. Although the conductor's punches are nowhere near the Metrocard's strip, the holes in the card prevent it from being inserted into a Metrocard vending machine or a station agent's machine to add money to the card.
If you want a refillable Metrocard, I would suggest trying to purchase a "pre-valued" card at one of the newsstands in your JFK arrival terminal before you head over to the terminal's AirTrain station.