Normally, a dead battery does not deactivate the fobs. Try using the fob, then, slightly press throttle as you turn the key. If the motor comes alive, maintain throttle at slow RPM's while idling. You may just have reset the computer module, and it will take about 10 minutes of either driving moderately or idling before the car will idle without "foot input".
Other thought would be to "resync" the fobs. Unfortunately, not sure if I remember the procedure... but might just be a matter of pushing both buttons simulataneously? Can anyone help on this one?