I definitely wouldn't separate once bonded. To be honest, I never separate from the moment rabbits meet unless there's a definite sign that the bond is completely broken and unlikely to settle again. (eg, I broke River/Morning because of continued fighting until it was clear their differences were too great. Both girls are happily bonded in with other buns now.)
Would it be possible for you to semi-neutralise a space (ie get rid of Benji's smell, all his toys included.) and keep them in that when first home, and then slowly expand it until they are totally free range again? I think that's what I'd do.