Its normal (aircraft) practice to do so, yes - to stop engines - then refuel. You could refuel with the engine on, the risk is probably small - but the consequences are rather severe, to put in mildly. Those chaps Elf and Safe-T would not approve, these days....
The Air Start system was supposed to give 6 starts. Believe the tests at Norris Bros, before going North, did prove 6 starts, but only with repeated recharging of the system. I suspect 6 starts was Norris Bros 'wish - seems fair. But the actual hardware that they had (from another aircraft, not a Gnat - the K7 on-board system supplied by Rotax) simply didn't actually do that. Oh well... Carry on, chaps....!
The numbers from Bill below, show that the 1st start could use up almost half the on-board air - ! Not great....
IanM