Rabbits shouldn't need their scent glands cleaned at all unless recommended by the vet. Routine cleaning can increase risk of infection to the scent glands and increase the risk of impaction.
In terms of aggression it's most likely;
1) they smell different
2) they've just given off a massive smell of territory marking scent which may aggravate the dominant bunny
3) the one that's had it done may be aggravated over the experience and is taking it out on their mates
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