There could be a few things going on here. Once a rabbit is spayed/neutered their smell and personality can change. Dad likely senses something is different about the baby and it may be confusing him into thinking the baby isn't the same rabbit.
It could also be a space issue. Are all three rabbits kept together in the cage at night and does the cage have plenty of space for them to run about and get away from each other if needed? If it is happening primarily in the cage and the cage lacks sufficient space for the rabbits to move about and get away from each other, this can sometimes cause an escalation of tension. Or if it's happening primarily when they are out free roaming but not when locked up for the night, it can sometimes be an issue of too much space. Basically they can get too far apart from each other for too long of a period and this can sometimes cause them to 'forget' each other, especially with the baby being newly neutered and likely smelling different.
If it's primarily in the cage it's happening, I would consider expanding their cage space. If it's primarily happening free roaming, I would consider restricting their free roaming space to a smaller area so they can maintain proximity and contact, until they seem truly bonded again and then only gradually reexpand their space. If it's both situations, it may be needed to rebond them going through the actual bonding process(slow or fast method). Either now if the bonding seems to go well, or if there still seem to be problems then separating the baby and dad for several weeks for the babies hormones to die down first, then trying rebonding then.
One thing you should be aware of and cautious of is the head butting is essentially the dad trying to run the baby off. This is an aggressive move(even if it may be because the dad is mistakenly thinking the baby is an intruder) and could potentially escalate into an attack that causes serious injury. So I would be very cautious of monitoring interactions and/or rebonding very carefully. The dad may never do more than the head butting until you resolve the bonding issue with them, but it's important to be aware that it is aggression and there is the potential for it to escalate.
These links have info on bonding. You may also be able to find a local rabbit rescue that is experienced with rabbit bonding that you could consult with.
https://www.cottontails-rescue.org.uk/information/bonding-bunnies/
http://www.saveabunny.org/rabbitcare/bonding-guide