I would not think that keeping him in the refugium would be any different than leaving him in the main display tank since the water is cycling through the whole system. The parasite will just be able to spread throughout the whole system. However, sometimes with a good feeding regime and limiting stress you can prevent an outbreak even with the parasite in the system. Unless you were going to treat I would probably leave him where he is to limit stress, but I know that others have different outlooks on ich.