I could see room for interpretation of this situation. The rules state:
Parry: Swords offer an excellent balance of defence and offence. A
model armed with a sword may parry blows. When his opponent rolls to hit, the model armed with a sword may roll a D6. If the score is greater than the highest to hit score of his opponent, the model has parried the blow, and that attack is discarded. A model may not parry attacks made with double or more its own Strength – they are simply too powerful to be stopped.
So, is the to hit score different from the to hit roll? Granted we are splitting hairs here, and I tend to favour interpretations that simplify game play over having to remember all kinds of exceptions (so personally I would go with natural rolls), but if a Plague Bearer's Cloud of Flies is supposed to distract and weaken the attacks of opponents, would this not make an opponent's attack easier to parry?