Alistair,
If the guide star is lost, I think it moves to the next item in the action list. I'm not 100% sure -- I can't find anything in the manual, and, I haven't encountered this problem yet.
The good news, though, is, that last night, I encountered my first automated run meridian flip. It worked beautifully.
Woke up this morning to find the scope parked. It then, woke up and went and did automatic sky flats at dawn, shut down the cooler and re-parked itself.
H