surely any disputed votes should have been isolated and considered openly at the count?
Well yes, but we don't know that they weren't considered openly at the count and then allocated because the voting intention was clear. In this case there would be no need to isolate them.
Surely if this petition is to go anywhere all 47000 votes now need to be rexamined?
And this, because of the huge expense, is exactly what the judge will be trying to avoid...