When you said you separate them what do you mean exactly? Do you take them out of the bonding situation entirely? If you do, I would recommend NOT doing that. Taking them away from each other teaches them that nipping/chasing will get them what they want (out of the situation). It can actually encourage aggressive behavior.
What I would do is do sessions in a smaller, portable, area. Like a box or laundry basket. When the nip/chasing starts shake the basket/box for a couple seconds which should make them stop. Another thing you can do is pet both firmly with each hand and alternating hands when they go nose to nose. This usually keeps them kind of “pressed down” to the floor and it distracts them a bit. I’ve done this in a lot in tense situations where a fight may break out with success.
Any time you physically take one rabbit away from another and end the session you want it to be on a good note. Even if the best moment you can get from them is laying nose to nose without fighting. 