Oh my, you might want to read up on bonding rabbits.
Though most of what you'll find is about neutered rabbits, it's worth a read anyway.
I keep my breeding does in pairs, but they are all mother/daughter pairs, so no experience with bonding, just that I wouldn't have the nerve to try to bring my two pairs together, they accidentially got in the garden at the same time several times, there were tufts of fur (never black fur from my small Fury), but they have 200m² with a lot of obstacles and holes to get out of sight of each other. I'm quite surprised that it worked well the first time you tried, and would deem that as a good sign.
I'm very relectant to seperate my pairs, there are sometimes troubles when putting them together again. Imho it's that "Oh, someone is invading MY place" that causes problems. When the other doe is always there, well, there are tensions at times, but they can deal with that. Just humping, chasing, tufts of fur, no real fights. I only separate when one, or both does are about to give birth, they aren't too interested in social issues then, and appreciate some rest and privacy - and their very own nest box. They have garden time together, but are seperated in the hutch then. Each has her own hutch, they are connected via tunnels.
When putting them together do that in a neutral space where none of them has been before. Can't tell if having babies does have an effect (it actually is more peacefully in my hutches when there are kits around, best thing is to breed both does at the same time, but that is settling into a familiar relationship)
That is not an expert opinion, but I would seperate them for at least a month or until the kits are weaned and away, introduce them again on neutral ground, and keep them there for at least some days if it works out.