Don't understand why the organisers would accept for 600 and reject for 1000. There's still the same amount of bikes circulating in practice as she can't ride them both at once.

If you are going to grant an entry to someone in the 600 class you might as well grant them entries to the others they wish to enter also. Then in the case she (or he) laps quick enough in qualifying they get to enter the race and if they don't they dont.